*******> update.16 Author: Taisung Lee, Darrin York, Charlie Lin Date: August 30, 2019 Programs: pmemd Description: Changes the way that softcore 14 interactions are handled. See http://ambermd.org/SC14_explanation.php -------------------------------------------------------------------------------- src/pmemd/src/cuda/gti_f95.cpp | 4 +- src/pmemd/src/cuda/gti_f95.h | 2 +- src/pmemd/src/cuda/gti_gpuContext.cpp | 4 +- src/pmemd/src/cuda/gti_gpuContext.h | 2 +- src/pmemd/src/cuda/gti_nonBond_kernels.cu | 160 +- src/pmemd/src/cuda/gti_simulationConst.h | 2 + src/pmemd/src/extra_pnts_nb14.i | 11 +- src/pmemd/src/mdin_ctrl_dat.F90 | 26 +- src/pmemd/src/pmemd.F90 | 2 +- test/cuda/Makefile | 36 +- .../gti/AFE_MBAR/softcore/complex/complex.out.DPFP | 411 +- .../gti/AFE_MBAR/softcore/complex/complex.out.SPFP | 396 +- .../gti/AFE_TI/softcore/complex/complex.out.DPFP | 325 +- test/cuda/gti/SC_Correction/complex/Run.SC_NVE | 98 + test/cuda/gti/SC_Correction/complex/Run.SC_NVT | 98 + .../cuda/gti/SC_Correction/complex/Run.SC_NVT_MBAR | 102 + test/cuda/gti/SC_Correction/complex/inpcrd | 41629 ++++++++ .../SC_Correction/complex/md_SC_NVE_SC_-1.o.DPFP | 2611 + .../SC_Correction/complex/md_SC_NVE_SC_-1.o.SPFP | 2617 + .../SC_Correction/complex/md_SC_NVE_SC_0.o.DPFP | 2588 + .../SC_Correction/complex/md_SC_NVE_SC_0.o.SPFP | 2617 + .../SC_Correction/complex/md_SC_NVE_SC_1.o.DPFP | 2611 + .../SC_Correction/complex/md_SC_NVE_SC_1.o.SPFP | 2617 + .../SC_Correction/complex/md_SC_NVE_SC_2.o.DPFP | 2611 + .../SC_Correction/complex/md_SC_NVE_SC_2.o.SPFP | 2617 + .../complex/md_SC_NVT_MBAR_SC_-1.o.DPFP | 3373 + .../complex/md_SC_NVT_MBAR_SC_-1.o.SPFP | 3379 + .../complex/md_SC_NVT_MBAR_SC_0.o.DPFP | 3373 + .../complex/md_SC_NVT_MBAR_SC_0.o.SPFP | 3379 + .../complex/md_SC_NVT_MBAR_SC_1.o.DPFP | 3373 + .../complex/md_SC_NVT_MBAR_SC_1.o.SPFP | 3379 + .../complex/md_SC_NVT_MBAR_SC_2.o.DPFP | 3373 + .../complex/md_SC_NVT_MBAR_SC_2.o.SPFP | 3379 + .../SC_Correction/complex/md_SC_NVT_SC_-1.o.DPFP | 2611 + .../SC_Correction/complex/md_SC_NVT_SC_-1.o.SPFP | 2617 + .../SC_Correction/complex/md_SC_NVT_SC_0.o.DPFP | 2588 + .../SC_Correction/complex/md_SC_NVT_SC_0.o.SPFP | 2617 + .../SC_Correction/complex/md_SC_NVT_SC_1.o.DPFP | 2611 + .../SC_Correction/complex/md_SC_NVT_SC_1.o.SPFP | 2617 + .../SC_Correction/complex/md_SC_NVT_SC_2.o.DPFP | 2611 + .../SC_Correction/complex/md_SC_NVT_SC_2.o.SPFP | 2617 + test/cuda/gti/SC_Correction/complex/mdcrd | 1 + test/cuda/gti/SC_Correction/complex/prmtop | 97386 +++++++++++++++++++ test/cuda/gti/SC_Correction/ligand/Run.SC_NVE | 98 + test/cuda/gti/SC_Correction/ligand/Run.SC_NVT | 97 + test/cuda/gti/SC_Correction/ligand/Run.SC_NVT_MBAR | 101 + test/cuda/gti/SC_Correction/ligand/inpcrd | 4773 + .../SC_Correction/ligand/md_SC_NVE_SC_-1.o.DPFP | 2612 + .../SC_Correction/ligand/md_SC_NVE_SC_-1.o.SPFP | 2618 + .../gti/SC_Correction/ligand/md_SC_NVE_SC_0.o.DPFP | 2589 + .../gti/SC_Correction/ligand/md_SC_NVE_SC_0.o.SPFP | 2618 + .../gti/SC_Correction/ligand/md_SC_NVE_SC_1.o.DPFP | 2612 + .../gti/SC_Correction/ligand/md_SC_NVE_SC_1.o.SPFP | 2618 + .../gti/SC_Correction/ligand/md_SC_NVE_SC_2.o.DPFP | 2612 + .../gti/SC_Correction/ligand/md_SC_NVE_SC_2.o.SPFP | 2618 + .../ligand/md_SC_NVT_MBAR_SC_-1.o.DPFP | 3373 + .../ligand/md_SC_NVT_MBAR_SC_-1.o.SPFP | 3379 + .../ligand/md_SC_NVT_MBAR_SC_0.o.DPFP | 3350 + .../ligand/md_SC_NVT_MBAR_SC_0.o.SPFP | 3379 + .../ligand/md_SC_NVT_MBAR_SC_1.o.DPFP | 3373 + .../ligand/md_SC_NVT_MBAR_SC_1.o.SPFP | 3379 + .../ligand/md_SC_NVT_MBAR_SC_2.o.DPFP | 3373 + .../ligand/md_SC_NVT_MBAR_SC_2.o.SPFP | 3379 + .../SC_Correction/ligand/md_SC_NVT_SC_-1.o.DPFP | 2611 + .../SC_Correction/ligand/md_SC_NVT_SC_-1.o.SPFP | 2617 + .../gti/SC_Correction/ligand/md_SC_NVT_SC_0.o.DPFP | 2588 + .../gti/SC_Correction/ligand/md_SC_NVT_SC_0.o.SPFP | 2617 + .../gti/SC_Correction/ligand/md_SC_NVT_SC_1.o.DPFP | 2611 + .../gti/SC_Correction/ligand/md_SC_NVT_SC_1.o.SPFP | 2617 + .../gti/SC_Correction/ligand/md_SC_NVT_SC_2.o.DPFP | 2611 + .../gti/SC_Correction/ligand/md_SC_NVT_SC_2.o.SPFP | 2617 + test/cuda/gti/SC_Correction/ligand/mdcrd | 1 + test/cuda/gti/SC_Correction/ligand/prmtop | 9933 ++ .../SC_Correction/methane_2_methanol/Run.NVT_ntt3 | 70 + .../gti/SC_Correction/methane_2_methanol/inpcrd | 1063 + .../methane_2_methanol/md_NVT_ntt3_SC_-1.o.DPFP | 632 + .../methane_2_methanol/md_NVT_ntt3_SC_-1.o.SPFP | 633 + .../methane_2_methanol/md_NVT_ntt3_SC_0.o.DPFP | 632 + .../methane_2_methanol/md_NVT_ntt3_SC_0.o.SPFP | 633 + .../methane_2_methanol/md_NVT_ntt3_SC_1.o.DPFP | 632 + .../methane_2_methanol/md_NVT_ntt3_SC_1.o.SPFP | 633 + .../methane_2_methanol/md_NVT_ntt3_SC_2.o.DPFP | 632 + .../methane_2_methanol/md_NVT_ntt3_SC_2.o.SPFP | 633 + .../gti/SC_Correction/methane_2_methanol/prmtop | 4314 + test/cuda/gti/complex/md_SC_NVE.o.DPFP | 81 +- test/cuda/gti/complex/md_SC_NVE.o.SPFP | 1260 +- test/cuda/gti/complex/md_SC_NVT.o.DPFP | 81 +- test/cuda/gti/complex/md_SC_NVT.o.SPFP | 1344 +- test/cuda/gti/complex/md_SC_NVT_MBAR.o.DPFP | 3302 +- 89 files changed, 404289 insertions(+), 98404 deletions(-) diff --git src/pmemd/src/cuda/gti_f95.cpp src/pmemd/src/cuda/gti_f95.cpp index 1696a5af19..569c5612e0 100644 --- src/pmemd/src/cuda/gti_f95.cpp +++ src/pmemd/src/cuda/gti_f95.cpp @@ -60,12 +60,12 @@ extern "C" void gti_init_md_parameters_(double* vlimit) //--------------------------------------------------------------------------------------------- extern "C" void gti_init_ti_parameters_(int ti_latm_lst[][3], int ti_lst[][3], int ti_sc_lst[], double* plambda, unsigned* pklambda, double* pscalpha, - double* pscbeta) + double* pscbeta, int* pAddSC) { gpuContext gpu = theGPUContext::GetPointer(); gpu->InitAccumulators(); gpu->InitTIParameters(ti_latm_lst, ti_lst, ti_sc_lst, *plambda, *pklambda, *pscalpha, - *pscbeta); + *pscbeta, *pAddSC); } //--------------------------------------------------------------------------------------------- diff --git src/pmemd/src/cuda/gti_f95.h src/pmemd/src/cuda/gti_f95.h index 55f98ea671..f451c50669 100644 --- src/pmemd/src/cuda/gti_f95.h +++ src/pmemd/src/cuda/gti_f95.h @@ -19,7 +19,7 @@ extern "C" void gti_init_md_parameters_(double* vlimit); extern "C" void gti_init_ti_parameters_(int ti_latm_lst[][3], int ti_lst[][3], int ti_sc_lst[], double* lambda, unsigned* klambda, double* scalpha, - double* scbeta); + double* scbeta, int* addSC); extern "C" void gti_build_nl_list_(int* ti_moode, int* lj1264); diff --git src/pmemd/src/cuda/gti_gpuContext.cpp src/pmemd/src/cuda/gti_gpuContext.cpp index 22fe2b61b9..94b04a2095 100644 --- src/pmemd/src/cuda/gti_gpuContext.cpp +++ src/pmemd/src/cuda/gti_gpuContext.cpp @@ -204,7 +204,7 @@ void gti_gpuContext::InitAccumulators() //--------------------------------------------------------------------------------------------- void gti_gpuContext::InitTIParameters(int ti_latm_lst[][3], int ti_lst[][3], int ti_sc_lst[], double lambda, unsigned klambda, double scalpha, - double scbeta) + double scbeta, int addSC) { // TI part pbTIList = new GpuBuffer(sim.stride3); @@ -307,6 +307,8 @@ void gti_gpuContext::InitTIParameters(int ti_latm_lst[][3], int ti_lst[][3], int sim.TIPrefactor = klambda* pow((1.0 - lambda), klambda-1); sim.TISCAlpha = scalpha; sim.TISCBeta = scbeta; + sim.addSC = addSC; + pbOrigAtomCharge = new GpuBuffer(sim.stride); sim.pOrigAtomCharge = pbOrigAtomCharge->_pDevData; } diff --git src/pmemd/src/cuda/gti_gpuContext.h src/pmemd/src/cuda/gti_gpuContext.h index b9cce7f4b4..8e25e82916 100644 --- src/pmemd/src/cuda/gti_gpuContext.h +++ src/pmemd/src/cuda/gti_gpuContext.h @@ -20,7 +20,7 @@ public: void InitMDParameters(double vlimit); void InitAccumulators(); void InitTIParameters(int ti_latm_lst[][3], int ti_lst[][3], int ti_sc_lst[], double lambda, - unsigned klambda, double scalpha, double scbeta); + unsigned klambda, double scalpha, double scbeta, int addSC); void InitMBARParameters(unsigned nMAR_state, double MBAR_lambda[][2]); void UpdateTICharges(double charge[]); void UpdateTIMasses(double mass[]); diff --git src/pmemd/src/cuda/gti_nonBond_kernels.cu src/pmemd/src/cuda/gti_nonBond_kernels.cu index c41a96ead9..6f88e5f1c2 100644 --- src/pmemd/src/cuda/gti_nonBond_kernels.cu +++ src/pmemd/src/cuda/gti_nonBond_kernels.cu @@ -246,12 +246,13 @@ _kPlainHead_ kgCalculateTINB_kernel(bool needEnergy, bool needVirial) { // energy: // needVirial: //--------------------------------------------------------------------------------------------- -_kPlainHead_ kgCalculateTI14NB_kernel(bool energy, bool needVirial) { +_kPlainHead_ kgCalculateTI14NB_kernel(bool needEnergy, bool needVirial) { unsigned int pos = (blockIdx.x * blockDim.x) + threadIdx.x; - unsigned long long int *pE0, *pE; - TIForce *pFx, *pFy, *pFz; + unsigned long long int* pE0, * pE; + TIForce* pFx, * pFy, * pFz; bool useSC14 = false; + while (pos < cSim.numberTI14NBEntries) { unsigned atom0 = cSim.pTINb14ID[pos].x; unsigned atom1 = cSim.pTINb14ID[pos].y; @@ -266,69 +267,72 @@ _kPlainHead_ kgCalculateTI14NB_kernel(bool energy, bool needVirial) { PMEDouble dx = cSim.pImageX[iatom1] - cSim.pImageX[iatom0]; PMEDouble dy = cSim.pImageY[iatom1] - cSim.pImageY[iatom0]; PMEDouble dz = cSim.pImageZ[iatom1] - cSim.pImageZ[iatom0]; - PMEDouble r2 = dx*dx + dy*dy + dz*dz; - PMEDouble rinv = rsqrt(r2); - PMEDouble r2inv = rinv*rinv; - PMEDouble df = 0.0; - PMEDouble t6 = 0.0; + PMEDouble r2 = dx * dx + dy * dy + dz * dz; + PMEDouble rinv = Rsqrt(r2); + PMEDouble r2inv = rinv * rinv; + PMEDouble df = ZeroF; + PMEDouble t6 = ZeroF; + bool isIntSC = (cSim.pSCList[atom0] > 0 && cSim.pSCList[atom1] > 0); bool hasSC = (cSim.pSCList[atom0] > 0 || cSim.pSCList[atom1] > 0); + bool addToDVDL_ele = false, addToDVDL_vdw = false; + + switch (cSim.addSC) { + case 0: addToDVDL_ele = (!hasSC); addToDVDL_vdw = (!hasSC); break; // only non-SC part + case 1: addToDVDL_ele = (!isIntSC); addToDVDL_vdw = (!isIntSC); break; // add common-SC (ele+vdw) boundary + case 2: addToDVDL_ele = true; addToDVDL_vdw = (!isIntSC); break; // add SC internal terms (ele only) + case -1: addToDVDL_ele = (!isIntSC); addToDVDL_vdw = (!hasSC); break; // add common-SC (ele only) boundary + } // EED: note that 1:4 electrostatics are double-counted - PMEDouble de = 0.0; + PMEDouble dE = 0.0; PMEDouble ddf = 0.0; + PMEDouble den =0.0 , den_n = 0.0; if (useSC14) { - PMEDouble den = rsqrt(r2 + (cSim.TISCBeta * cSim.TILambda[TIRegion])); - de = g1 * den; - PMEDouble den_n = powf(den, 3.0); + den = Rsqrt(r2 + (cSim.TISCBeta * cSim.TILambda[TIRegion])); + dE = g1 * den; + den_n = powf(den, 3.0); ddf = g1 * den_n; - de = 0.5 * g1 * den_n * cSim.TISCBeta * TISign; } else { - de = g1 * rinv; - ddf = de * r2inv; - } - pE = (hasSC) ? cSim.pSCEE14[TIRegion] : cSim.pTIEE14[TIRegion]; - pE0 = cSim.pTIEE14[2]; - addEnergy(pE, de); - if (!hasSC) { - addEnergy(pE0, -de); + dE = g1 * rinv; + ddf = dE * r2inv; } df += ddf; - // EVDW: note that 14 NB is not double-counted since it is zeroed-out - t6 = r2inv * r2inv * r2inv; - f6 *= g2 * t6; - f12 *= g2 * t6 * t6; - de = f12 - f6; - ddf = OneF; - if (useSC14) { - PMEDouble sig_6 = f6 / f12; - PMEDouble fourEps = f6 * sig_6; - t6 = r2 * r2 * r2 * sig_6; - f6 = OneF / ((cSim.TISCAlpha * cSim.TILambda[TIRegion]) + t6); - f12 = f6 * f6; - ddf = fourEps * f6 * t6; - } - ddf *= (f12*SixF - f6*ThreeF) * TwoF * r2inv; - pE = (hasSC) ? cSim.pSCLJ14[TIRegion] : cSim.pTILJ14[TIRegion]; - pE0 = cSim.pTILJ14[2]; - addEnergy(pE, de); + if (needEnergy) { + pE = (addToDVDL_ele) ? cSim.pTIEE14[TIRegion] : cSim.pSCEE14[TIRegion]; + addEnergy(pE, dE); - // Add to the force accumulators - if (hasSC) { - pFx = cSim.pTINBSCForceX[TIRegion]; - pFy = cSim.pTINBSCForceY[TIRegion]; - pFz = cSim.pTINBSCForceZ[TIRegion]; - } else { + if (addToDVDL_ele) { + pE0 = cSim.pTIEE14[2]; + addEnergy(pE0, -dE); + + if (useSC14){ + PMEFloat dl = 0.5 * g1 * den_n * cSim.TISCBeta * TISign; + addEnergy(cSim.pTISCEED_DL[TIRegion], dl); + + if (cSim.needMBAR) { + for (unsigned l = 0; l < cSim.nMBARStates; l++) { + PMEDouble den_n = Rsqrt(r2 + cSim.TISCBeta * cSim.MBARLambda[TIRegion][l]); + addEnergy(&(cSim.pMBAREnergy[l]), + g1 * (OneF - cSim.MBARLambda[TIRegion][l]) * (den_n - den)); + } + + } + } + } + } + + if (addToDVDL_ele) { pFx = cSim.pTINBForceX[TIRegion]; pFy = cSim.pTINBForceY[TIRegion]; pFz = cSim.pTINBForceZ[TIRegion]; + } else { + pFx = cSim.pTINBSCForceX[TIRegion]; + pFy = cSim.pTINBSCForceY[TIRegion]; + pFz = cSim.pTINBSCForceZ[TIRegion]; } - // Add to the force accumulators - PMEDouble df0 = df; // Ele only - df += ddf; // Ele and vDW - PMEFloat ttx = df * dx; PMEFloat tty = df * dy; PMEFloat ttz = df * dz; @@ -338,16 +342,16 @@ _kPlainHead_ kgCalculateTI14NB_kernel(bool energy, bool needVirial) { addForce(pFy + iatom1, tty); addForce(pFz + iatom0, -ttz); addForce(pFz + iatom1, ttz); - if (needVirial && !isIntSC) { + if (needVirial && addToDVDL_ele) { addVirial(cSim.pV11[TIRegion], -ttx * dx); addVirial(cSim.pV22[TIRegion], -tty * dy); addVirial(cSim.pV33[TIRegion], -ttz * dz); } // Correction for double-counted 1-4 ele - ttx = df0 * dx; - tty = df0 * dy; - ttz = df0 * dz; + ttx = df * dx; + tty = df * dy; + ttz = df * dz; addForce(cSim.pTINBForceX[2] + iatom0, ttx); addForce(cSim.pTINBForceX[2] + iatom1, -ttx); addForce(cSim.pTINBForceY[2] + iatom0, tty); @@ -359,10 +363,60 @@ _kPlainHead_ kgCalculateTI14NB_kernel(bool energy, bool needVirial) { addVirial(cSim.pVirial_22, tty * dy); addVirial(cSim.pVirial_33, ttz * dz); } + + df = OneF; // df must be 1.0 here + // EVDW: note that 14 NB is not double-counted since it is zeroed-out + t6 = r2inv * r2inv * r2inv; + f6 *= g2 * t6; + f12 *= g2 * t6 * t6; + dE = f12 - f6; + + if (useSC14) { + PMEDouble sig_6 = f6 / f12; + PMEDouble fourEps = f6 * sig_6; + t6 = r2 * r2 * r2 * sig_6; + f6 = OneF / ((cSim.TISCAlpha * cSim.TILambda[TIRegion]) + t6); + f12 = f6 * f6; + df = fourEps * f6 * t6; + } + df *= (f12 * SixF - f6 * ThreeF) * TwoF * r2inv; + + if (needEnergy) { + pE = (addToDVDL_vdw) ? cSim.pTILJ14[TIRegion] : cSim.pSCLJ14[TIRegion]; + addEnergy(pE, dE); + } + + // Add to the force accumulators + if (addToDVDL_vdw) { + pFx = cSim.pTINBForceX[TIRegion]; + pFy = cSim.pTINBForceY[TIRegion]; + pFz = cSim.pTINBForceZ[TIRegion]; + } else { + pFx = cSim.pTINBSCForceX[TIRegion]; + pFy = cSim.pTINBSCForceY[TIRegion]; + pFz = cSim.pTINBSCForceZ[TIRegion]; + } + + ttx = df * dx; + tty = df * dy; + ttz = df * dz; + addForce(pFx + iatom0, -ttx); + addForce(pFx + iatom1, ttx); + addForce(pFy + iatom0, -tty); + addForce(pFy + iatom1, tty); + addForce(pFz + iatom0, -ttz); + addForce(pFz + iatom1, ttz); + if (needVirial && addToDVDL_vdw) { + addVirial(cSim.pV11[TIRegion], -ttx * dx); + addVirial(cSim.pV22[TIRegion], -tty * dy); + addVirial(cSim.pV33[TIRegion], -ttz * dz); + } + pos += gridDim.x * blockDim.x; } } + //--------------------------------------------------------------------------------------------- // kgCalculate1264NB_kernel: // diff --git src/pmemd/src/cuda/gti_simulationConst.h src/pmemd/src/cuda/gti_simulationConst.h index 5f355ee65c..f726a3189d 100644 --- src/pmemd/src/cuda/gti_simulationConst.h +++ src/pmemd/src/cuda/gti_simulationConst.h @@ -30,6 +30,8 @@ public: unsigned TIk; double TISCAlpha, TISCBeta, TIPrefactor, TILambda[2], TIWeight[2]; + int addSC; // 1: add boundary 1-4; 2: add all internal elec + unsigned *pTIList; // Original TI list from pmemd unsigned *pSCList; // Original TI list from pmemd diff --git src/pmemd/src/extra_pnts_nb14.i src/pmemd/src/extra_pnts_nb14.i index 940274bb20..608b76e972 100644 --- src/pmemd/src/extra_pnts_nb14.i +++ src/pmemd/src/extra_pnts_nb14.i @@ -3,7 +3,7 @@ use ti_mod use phmd_mod !PHMD - use mdin_ctrl_dat_mod, only : iphmd + use mdin_ctrl_dat_mod, only : iphmd, gti_add_sc !PHMD implicit none @@ -119,8 +119,13 @@ if (ti_region .gt. 0) then if (ti_mode .ne. 1) then - ti_lscale = (ti_sc_lst(i) .lt. 2 .and. & - ti_sc_lst(j) .lt. 2) + if(gti_add_sc .eq. 1) then + ti_lscale = (ti_sc_lst(i) .lt. 2 .or. & + ti_sc_lst(j) .lt. 2) + else + ti_lscale = (ti_sc_lst(i) .lt. 2 .and. & + ti_sc_lst(j) .lt. 2) + end if end if #ifdef MPI #ifdef GBorn diff --git src/pmemd/src/mdin_ctrl_dat.F90 src/pmemd/src/mdin_ctrl_dat.F90 index e284620fae..261a74b89e 100644 --- src/pmemd/src/mdin_ctrl_dat.F90 +++ src/pmemd/src/mdin_ctrl_dat.F90 @@ -45,7 +45,7 @@ use file_io_dat_mod ineb, skmin, skmax, tmode, vv, nebfreq, & irandom, mask_from_ref, mbar_states, & geq_nstep, ginit_vel, gsyn_mass, & !GTI - gremd_acyc, gti_cpu_output, & ! GTI + gremd_acyc, gti_cpu_output, gti_add_sc, & ! GTI midpoint character(4) ihwtnm(2), iowtnm, iwtnm @@ -74,12 +74,12 @@ use file_io_dat_mod icnste,ntcnste,ntrelaxe, & ! 94 mask_from_ref, mbar_states, & ! 96 geq_nstep, ginit_vel, gsyn_mass, & !99 - gremd_acyc, gti_cpu_output, & !101 - mcint,nmd,mcrescyc,nmc,mcverbosity, & !106 - ineb,skmin,skmax,tmode,vv, nebfreq, & !112 - iphmd, midpoint !114 + gremd_acyc, gti_cpu_output, gti_add_sc, & !102 + mcint,nmd,mcrescyc,nmc,mcverbosity, & !107 + ineb,skmin,skmax,tmode,vv,nebfreq, & !113 + iphmd, midpoint !115 - integer, parameter :: mdin_ctrl_int_cnt = 114 + integer, parameter :: mdin_ctrl_int_cnt = 115 save :: / mdin_ctrl_int / @@ -302,9 +302,10 @@ use file_io_dat_mod efx,efy,efz,efn,effreq,efphase,infe,irandom, & mbar_lambda, mbar_states, mask_from_ref, & geq_nstep, ginit_vel, gsyn_mass, gremd_acyc, & - gti_cpu_output,mcwat,nmd,mcint,nmc,mcrescyc,mcverbosity,& - mcresstr,mcwatmaxdif,ineb,skmin,skmax,tmode,vv,vfac,nebfreq,& - mcboxshift, midpoint + gti_cpu_output, gti_add_sc, & + mcwat,nmd,mcint,nmc,mcrescyc,mcverbosity,& + mcresstr,mcwatmaxdif,ineb,skmin,skmax,tmode,vv,vfac,& + nebfreq, mcboxshift, midpoint contains @@ -659,6 +660,7 @@ subroutine init_mdin_ctrl_dat(remd_method) gremd_acyc = 1 gti_cpu_output =1 #endif + gti_add_sc = 1 ! MBAR ifmbar = 0 @@ -2109,6 +2111,12 @@ subroutine validate_mdin_ctrl_dat(remd_method) write(mdout, '(a,a)') error_hdr, 'Set klambda between 1 and 6!' inerr = 1 end if +#ifdef CUDA + if (igb .ne. 0) then + write(mdout, '(a,a)') error_hdr, 'TI is incompatible with GB on GPU' + inerr = 1 + end if +#endif if (ips .ne. 0) then write(mdout, '(a,a)') error_hdr, 'TI is incompatible with IPS' inerr = 1 diff --git src/pmemd/src/pmemd.F90 src/pmemd/src/pmemd.F90 index e553fc2feb..ce102e0325 100644 --- src/pmemd/src/pmemd.F90 +++ src/pmemd/src/pmemd.F90 @@ -424,7 +424,7 @@ if (terminal_flag) call mexit(6,0) if (ti_mode .ne. 0) then !call gti_add_ti_to_exclusion(natom, atm_numex, size(gbl_natex), gbl_natex) call gti_init_ti_parameters(ti_latm_lst, ti_lst, ti_sc_lst, & - clambda, klambda, scalpha, scbeta); + clambda, klambda, scalpha, scbeta, gti_add_sc); if (ifmbar .ne. 0) call gti_init_mbar_parameters(bar_states, bar_lambda) endif diff --git test/cuda/Makefile test/cuda/Makefile index b264b61022..284fba627e 100644 --- test/cuda/Makefile +++ test/cuda/Makefile @@ -11,7 +11,7 @@ test.pmemd.cuda: test.pmemd.cuda.gb.serial test.pmemd.cuda.gb \ test.pmemd.cuda.gb.serial test.pmemd.cuda.gb \ test.pmemd.cuda.pme test.pmemd.cuda.pme.serial \ test.pmemd.cuda.pme.big \ - test.pmemd.cuda.$(FEP_MODE) + test.pmemd.cuda.$(FEP_MODE) test.pmemd.cuda.SC_Correction test.pmemd.cuda.MPI: test.pmemd.cuda.gb test.pmemd.cuda.pme test.pmemd.cuda.pme.big \ @@ -243,5 +243,39 @@ test.pmemd.cuda.gti: -cd gti/AFE_MBAR/softcore/complex && ./Run.complex $(PREC_MODEL) -cd gti/AFE_MBAR/softcore/electro && ./Run.electro $(PREC_MODEL) +test.pmemd.cuda.SC_Correction: +#Begin GTI Tests + @echo "------------------------------------" + @echo "Running CUDA GTI free energy SC correction tests." + -cd gti/SC_Correction/methane_2_methanol/ && SC_CORR=0 ./Run.NVT_ntt3 $(PREC_MODEL) + -cd gti/SC_Correction/methane_2_methanol/ && SC_CORR=-1 ./Run.NVT_ntt3 $(PREC_MODEL) + -cd gti/SC_Correction/methane_2_methanol/ && SC_CORR=1 ./Run.NVT_ntt3 $(PREC_MODEL) + -cd gti/SC_Correction/methane_2_methanol/ && SC_CORR=2 ./Run.NVT_ntt3 $(PREC_MODEL) + -cd gti/SC_Correction/ligand/ && SC_CORR=0 ./Run.SC_NVE $(PREC_MODEL) + -cd gti/SC_Correction/ligand/ && SC_CORR=-1 ./Run.SC_NVE $(PREC_MODEL) + -cd gti/SC_Correction/ligand/ && SC_CORR=1 ./Run.SC_NVE $(PREC_MODEL) + -cd gti/SC_Correction/ligand/ && SC_CORR=2 ./Run.SC_NVE $(PREC_MODEL) + -cd gti/SC_Correction/ligand/ && SC_CORR=0 ./Run.SC_NVT $(PREC_MODEL) + -cd gti/SC_Correction/ligand/ && SC_CORR=-1 ./Run.SC_NVT $(PREC_MODEL) + -cd gti/SC_Correction/ligand/ && SC_CORR=1 ./Run.SC_NVT $(PREC_MODEL) + -cd gti/SC_Correction/ligand/ && SC_CORR=2 ./Run.SC_NVT $(PREC_MODEL) + -cd gti/SC_Correction/ligand/ && SC_CORR=0 ./Run.SC_NVT_MBAR $(PREC_MODEL) + -cd gti/SC_Correction/ligand/ && SC_CORR=-1 ./Run.SC_NVT_MBAR $(PREC_MODEL) + -cd gti/SC_Correction/ligand/ && SC_CORR=1 ./Run.SC_NVT_MBAR $(PREC_MODEL) + -cd gti/SC_Correction/ligand/ && SC_CORR=2 ./Run.SC_NVT_MBAR $(PREC_MODEL) + -cd gti/SC_Correction/complex/ && SC_CORR=0 ./Run.SC_NVE $(PREC_MODEL) + -cd gti/SC_Correction/complex/ && SC_CORR=-1 ./Run.SC_NVE $(PREC_MODEL) + -cd gti/SC_Correction/complex/ && SC_CORR=1 ./Run.SC_NVE $(PREC_MODEL) + -cd gti/SC_Correction/complex/ && SC_CORR=2 ./Run.SC_NVE $(PREC_MODEL) + -cd gti/SC_Correction/complex/ && SC_CORR=0 ./Run.SC_NVT $(PREC_MODEL) + -cd gti/SC_Correction/complex/ && SC_CORR=-1 ./Run.SC_NVT $(PREC_MODEL) + -cd gti/SC_Correction/complex/ && SC_CORR=1 ./Run.SC_NVT $(PREC_MODEL) + -cd gti/SC_Correction/complex/ && SC_CORR=2 ./Run.SC_NVT $(PREC_MODEL) + -cd gti/SC_Correction/complex/ && SC_CORR=0 ./Run.SC_NVT_MBAR $(PREC_MODEL) + -cd gti/SC_Correction/complex/ && SC_CORR=-1 ./Run.SC_NVT_MBAR $(PREC_MODEL) + -cd gti/SC_Correction/complex/ && SC_CORR=1 ./Run.SC_NVT_MBAR $(PREC_MODEL) + -cd gti/SC_Correction/complex/ && SC_CORR=2 ./Run.SC_NVT_MBAR $(PREC_MODEL) + + #End Explicit Solvent Tests diff --git test/cuda/gti/AFE_MBAR/softcore/complex/complex.out.DPFP test/cuda/gti/AFE_MBAR/softcore/complex/complex.out.DPFP index ca80509112..c0e4ffa3db 100644 --- test/cuda/gti/AFE_MBAR/softcore/complex/complex.out.DPFP +++ test/cuda/gti/AFE_MBAR/softcore/complex/complex.out.DPFP @@ -1,14 +1,14 @@ ------------------------------------------------------- - Amber 16 PMEMD 2016 + Amber 18 PMEMD 2018 ------------------------------------------------------- -| PMEMD implementation of SANDER, Release 16 +| PMEMD implementation of SANDER, Release 18 -| Run on 02/13/2018 at 10:33:21 +| Run on 08/12/2019 at 14:12:44 -| Executable path: /home/taisung/amber/bin/pmemd.cuda_DPFP -| Working directory: /home/taisung/amber/test/cuda/gti/AFE_MBAR/softcore/complex +| Executable path: /usr/people/taisung/amber/amber_release/bin/pmemd.cuda_DPFP +| Working directory: /usr/people/taisung/amber/amber_release/test/cuda/gti/AFE_MBAR/softcore/complex | Hostname: Unknown [-O]verwriting output @@ -60,14 +60,17 @@ NPT test |--------------------- INFORMATION ---------------------- | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE. -| Version 16.0.0 +| Version 18.0.0 | -| 02/25/2016 +| 03/25/2018 | | Implementation by: | Ross C. Walker (SDSC) | Scott Le Grand (nVIDIA) | +| Version 18 performance extensions by: +| David Cerutti (Rutgers) +| | Precision model in use: | [DPFP] - Double Precision Forces, 64-bit Fixed point | Accumulation. @@ -93,17 +96,37 @@ NPT test | with AMBER - Part I: Generalized Born", J. Chem. | Theory Comput., 2012, 8 (5), pp1542-1555. | +| When publishing work that utilized the CUDA version +| of TI, BAR, MBAR or FEP please cite the following +| three publications in addition to the regular AMBER +| GPU citations: +| +| - Daniel J. Mermelstein; Charles Lin; Gard Nelson; +| Rachael Kretsch; J. Andrew McCammon; Ross C. Walker +| "Fast and Flexible GPU Accelerated Binding +| Free Energy Calculations within the AMBER Molecular +| Dynamics Package" J. Comp. Chem., 2018, +| DOI: 10.1002/jcc.25187 +| +| - Tai-Sung Lee; Yuan Hu; Brad Sherborne; Zhuyan Guo; +| Darrin M. York +| "Toward Fast and Accurate Binding Affinity Prediction with +| pmemdGTI: An Efficient Implementation of GPU-Accelerated +| Thermodynamic Integration" +| J. Chem. Theory Comput., 2017, 13 (7), 3077 +| +| |-------------------------------------------------------- |------------------- GPU DEVICE INFO -------------------- | -| CUDA_VISIBLE_DEVICES: not set +| CUDA_VISIBLE_DEVICES: 1 | CUDA Capable Devices Detected: 1 | CUDA Device ID in use: 0 -| CUDA Device Name: Tesla V100-PCIE-16GB -| CUDA Device Global Mem Size: 16152 MB +| CUDA Device Name: TITAN V +| CUDA Device Global Mem Size: 12066 MB | CUDA Device Num Multiprocessors: 80 -| CUDA Device Core Freq: 1.38 GHz +| CUDA Device Core Freq: 1.46 GHz | |-------------------------------------------------------- @@ -273,17 +296,17 @@ Total charge of -0.04433900 removed from 3 atoms SHAKE constraints in the SC region: 1 MBAR Energy analysis: -Energy at 0.0000 = -91165.0582 -Energy at 0.1000 = -91165.0729 -Energy at 0.2000 = -91165.0030 -Energy at 0.3000 = -91164.8642 -Energy at 0.4000 = -91164.6539 -Energy at 0.5000 = -91164.3541 -Energy at 0.6000 = -91163.9264 -Energy at 0.7000 = -91163.2974 -Energy at 0.8000 = -91162.3218 -Energy at 0.9000 = -91160.6825 -Energy at 1.0000 = -91157.5762 +Energy at 0.0000 = -91165.0734 +Energy at 0.1000 = -91165.0897 +Energy at 0.2000 = -91165.0215 +Energy at 0.3000 = -91164.8841 +Energy at 0.4000 = -91164.6753 +Energy at 0.5000 = -91164.3770 +Energy at 0.6000 = -91163.9508 +Energy at 0.7000 = -91163.3234 +Energy at 0.8000 = -91162.3493 +Energy at 0.9000 = -91160.7115 +Energy at 1.0000 = -91157.6069 ------------------------------------------------------------------------------ @@ -291,22 +314,22 @@ Energy at 1.0000 = -91157.5762 NSTEP = 5 TIME(PS) = 250.005 TEMP(K) = 297.20 PRESS = 0.0 - Etot = -73131.9810 EKtot = 18031.9454 EPtot = -91163.9264 - BOND = 508.4395 ANGLE = 1292.6930 DIHED = 1775.5200 - 1-4 NB = 611.4277 1-4 EEL = 6260.5475 VDWAALS = 11214.7368 - EELEC = -112827.2910 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73132.0199 EKtot = 18031.9309 EPtot = -91163.9508 + BOND = 508.4360 ANGLE = 1292.6994 DIHED = 1775.5194 + 1-4 NB = 611.3998 1-4 EEL = 6260.5455 VDWAALS = 11214.7395 + EELEC = -112827.2904 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0110 - DV/DL = 5.1188 + DV/DL = 5.1037 ------------------------------------------------------------------------------ - Softcore part of the system: 1 atoms, TEMP(K) = 613.51 - SC_Etot= 2.1681 SC_EKtot= 1.8287 SC_EPtot = 0.3394 - SC_BOND= 0.0000 SC_ANGLE= 0.0858 SC_DIHED = 0.2740 - SC_14NB= -0.0204 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 1 atoms, TEMP(K) = 613.46 + SC_Etot= 2.1892 SC_EKtot= 1.8286 SC_EPtot = 0.3606 + SC_BOND= 0.0000 SC_ANGLE= 0.0871 SC_DIHED = 0.2735 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6367 SC_DERIV = 2.6367 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6364 SC_DERIV = 2.6364 ------------------------------------------------------------------------------ @@ -314,37 +337,37 @@ Energy at 1.0000 = -91157.5762 NSTEP = 5 TIME(PS) = 250.005 TEMP(K) = 297.17 PRESS = 0.0 - Etot = -73133.2756 EKtot = 18030.6508 EPtot = -91163.9264 - BOND = 508.4395 ANGLE = 1292.6930 DIHED = 1775.5200 - 1-4 NB = 611.4277 1-4 EEL = 6260.5475 VDWAALS = 11214.7368 - EELEC = -112827.2910 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73133.3110 EKtot = 18030.6398 EPtot = -91163.9508 + BOND = 508.4360 ANGLE = 1292.6994 DIHED = 1775.5194 + 1-4 NB = 611.3998 1-4 EEL = 6260.5455 VDWAALS = 11214.7395 + EELEC = -112827.2904 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0111 - DV/DL = 5.1188 + DV/DL = 5.1037 ------------------------------------------------------------------------------ - Softcore part of the system: 2 atoms, TEMP(K) = 107.53 - SC_Etot= 1.7294 SC_EKtot= 0.5342 SC_EPtot = 1.1952 - SC_BOND= 0.0051 SC_ANGLE= 0.3800 SC_DIHED = 0.8451 - SC_14NB= -0.0350 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 2 atoms, TEMP(K) = 108.19 + SC_Etot= 1.7672 SC_EKtot= 0.5375 SC_EPtot = 1.2297 + SC_BOND= 0.0050 SC_ANGLE= 0.3801 SC_DIHED = 0.8446 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6367 SC_DERIV = 2.6367 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6364 SC_DERIV = 2.6364 ------------------------------------------------------------------------------ MBAR Energy analysis: -Energy at 0.0000 = -91438.4933 -Energy at 0.1000 = -91438.5543 -Energy at 0.2000 = -91438.4676 -Energy at 0.3000 = -91438.2826 -Energy at 0.4000 = -91438.0109 -Energy at 0.5000 = -91437.6402 -Energy at 0.6000 = -91437.1330 -Energy at 0.7000 = -91436.4110 -Energy at 0.8000 = -91435.3118 -Energy at 0.9000 = -91433.4664 -Energy at 1.0000 = -91429.8909 +Energy at 0.0000 = -91438.5733 +Energy at 0.1000 = -91438.6309 +Energy at 0.2000 = -91438.5403 +Energy at 0.3000 = -91438.3511 +Energy at 0.4000 = -91438.0751 +Energy at 0.5000 = -91437.7001 +Energy at 0.6000 = -91437.1886 +Energy at 0.7000 = -91436.4623 +Energy at 0.8000 = -91435.3589 +Energy at 0.9000 = -91433.5097 +Energy at 1.0000 = -91429.9311 ------------------------------------------------------------------------------ @@ -352,60 +375,60 @@ Energy at 1.0000 = -91429.8909 NSTEP = 10 TIME(PS) = 250.010 TEMP(K) = 301.64 PRESS = 0.0 - Etot = -73135.6505 EKtot = 18301.4825 EPtot = -91437.1330 - BOND = 463.1871 ANGLE = 1168.6040 DIHED = 1767.6816 - 1-4 NB = 609.6493 1-4 EEL = 6271.0879 VDWAALS = 11237.5061 - EELEC = -112954.8491 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73135.6553 EKtot = 18301.5333 EPtot = -91437.1886 + BOND = 463.1644 ANGLE = 1168.5709 DIHED = 1767.6810 + 1-4 NB = 609.6525 1-4 EEL = 6271.0817 VDWAALS = 11237.5091 + EELEC = -112954.8481 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0110 - DV/DL = 5.9672 + DV/DL = 6.0103 ------------------------------------------------------------------------------ - Softcore part of the system: 1 atoms, TEMP(K) = 473.73 - SC_Etot= 2.7419 SC_EKtot= 1.4121 SC_EPtot = 1.3298 - SC_BOND= 0.3561 SC_ANGLE= 0.0793 SC_DIHED = 0.9227 - SC_14NB= -0.0283 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 1 atoms, TEMP(K) = 473.87 + SC_Etot= 2.7762 SC_EKtot= 1.4125 SC_EPtot = 1.3637 + SC_BOND= 0.3577 SC_ANGLE= 0.0822 SC_DIHED = 0.9238 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6753 SC_DERIV = 2.6753 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6740 SC_DERIV = 2.6740 ------------------------------------------------------------------------------ | TI region 2 - NSTEP = 10 TIME(PS) = 250.010 TEMP(K) = 301.61 PRESS = 0.0 - Etot = -73136.6869 EKtot = 18300.4461 EPtot = -91437.1330 - BOND = 463.1871 ANGLE = 1168.6040 DIHED = 1767.6816 - 1-4 NB = 609.6493 1-4 EEL = 6271.0879 VDWAALS = 11237.5061 - EELEC = -112954.8491 EHBOND = 0.0000 RESTRAINT = 0.0000 + NSTEP = 10 TIME(PS) = 250.010 TEMP(K) = 301.62 PRESS = 0.0 + Etot = -73136.6845 EKtot = 18300.5040 EPtot = -91437.1886 + BOND = 463.1644 ANGLE = 1168.5709 DIHED = 1767.6810 + 1-4 NB = 609.6525 1-4 EEL = 6271.0817 VDWAALS = 11237.5091 + EELEC = -112954.8481 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0111 - DV/DL = 5.9672 + DV/DL = 6.0103 ------------------------------------------------------------------------------ - Softcore part of the system: 2 atoms, TEMP(K) = 75.62 - SC_Etot= 1.3827 SC_EKtot= 0.3757 SC_EPtot = 1.0070 - SC_BOND= 0.0460 SC_ANGLE= 0.4271 SC_DIHED = 0.5172 - SC_14NB= 0.0167 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 2 atoms, TEMP(K) = 77.14 + SC_Etot= 1.3730 SC_EKtot= 0.3832 SC_EPtot = 0.9898 + SC_BOND= 0.0466 SC_ANGLE= 0.4264 SC_DIHED = 0.5168 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6753 SC_DERIV = 2.6753 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6740 SC_DERIV = 2.6740 ------------------------------------------------------------------------------ MBAR Energy analysis: -Energy at 0.0000 = -91585.3558 -Energy at 0.1000 = -91585.3209 -Energy at 0.2000 = -91585.1932 -Energy at 0.3000 = -91584.9925 -Energy at 0.4000 = -91584.7176 -Energy at 0.5000 = -91584.3494 -Energy at 0.6000 = -91583.8450 -Energy at 0.7000 = -91583.1186 -Energy at 0.8000 = -91581.9921 -Energy at 0.9000 = -91580.0526 -Energy at 1.0000 = -91576.1624 +Energy at 0.0000 = -91585.3073 +Energy at 0.1000 = -91585.2566 +Energy at 0.2000 = -91585.1135 +Energy at 0.3000 = -91584.8975 +Energy at 0.4000 = -91584.6074 +Energy at 0.5000 = -91584.2241 +Energy at 0.6000 = -91583.7048 +Energy at 0.7000 = -91582.9639 +Energy at 0.8000 = -91581.8235 +Energy at 0.9000 = -91579.8715 +Energy at 1.0000 = -91575.9732 ------------------------------------------------------------------------------ @@ -413,22 +436,22 @@ Energy at 1.0000 = -91576.1624 NSTEP = 15 TIME(PS) = 250.015 TEMP(K) = 304.05 PRESS = 0.0 - Etot = -73136.5402 EKtot = 18447.3048 EPtot = -91583.8450 - BOND = 476.3551 ANGLE = 1266.8188 DIHED = 1746.6100 - 1-4 NB = 612.1279 1-4 EEL = 6282.3473 VDWAALS = 11264.0751 - EELEC = -113232.1791 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73136.3793 EKtot = 18447.3254 EPtot = -91583.7048 + BOND = 476.3874 ANGLE = 1266.8246 DIHED = 1746.6122 + 1-4 NB = 612.2341 1-4 EEL = 6282.3389 VDWAALS = 11264.0758 + EELEC = -113232.1778 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0110 - DV/DL = 5.9590 + DV/DL = 6.1065 ------------------------------------------------------------------------------ - Softcore part of the system: 1 atoms, TEMP(K) = 176.90 - SC_Etot= 2.8532 SC_EKtot= 0.5273 SC_EPtot = 2.3259 - SC_BOND= 0.6680 SC_ANGLE= 0.1005 SC_DIHED = 1.5510 - SC_14NB= 0.0064 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 1 atoms, TEMP(K) = 177.49 + SC_Etot= 2.8599 SC_EKtot= 0.5291 SC_EPtot = 2.3308 + SC_BOND= 0.6770 SC_ANGLE= 0.1016 SC_DIHED = 1.5522 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.7872 SC_DERIV = 2.7872 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.7835 SC_DERIV = 2.7835 ------------------------------------------------------------------------------ @@ -436,37 +459,37 @@ Energy at 1.0000 = -91576.1624 NSTEP = 15 TIME(PS) = 250.015 TEMP(K) = 304.03 PRESS = 0.0 - Etot = -73136.8874 EKtot = 18446.9576 EPtot = -91583.8450 - BOND = 476.3551 ANGLE = 1266.8188 DIHED = 1746.6100 - 1-4 NB = 612.1279 1-4 EEL = 6282.3473 VDWAALS = 11264.0751 - EELEC = -113232.1791 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73136.7191 EKtot = 18446.9856 EPtot = -91583.7048 + BOND = 476.3874 ANGLE = 1266.8246 DIHED = 1746.6122 + 1-4 NB = 612.2341 1-4 EEL = 6282.3389 VDWAALS = 11264.0758 + EELEC = -113232.1778 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0111 - DV/DL = 5.9590 + DV/DL = 6.1065 ------------------------------------------------------------------------------ - Softcore part of the system: 2 atoms, TEMP(K) = 36.26 - SC_Etot= 1.6537 SC_EKtot= 0.1801 SC_EPtot = 1.4736 - SC_BOND= 0.0058 SC_ANGLE= 0.5879 SC_DIHED = 0.7255 - SC_14NB= 0.1543 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 2 atoms, TEMP(K) = 38.09 + SC_Etot= 1.5080 SC_EKtot= 0.1893 SC_EPtot = 1.3188 + SC_BOND= 0.0067 SC_ANGLE= 0.5871 SC_DIHED = 0.7249 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.7872 SC_DERIV = 2.7872 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.7835 SC_DERIV = 2.7835 ------------------------------------------------------------------------------ MBAR Energy analysis: -Energy at 0.0000 = -91639.7616 -Energy at 0.1000 = -91639.7555 -Energy at 0.2000 = -91639.6762 -Energy at 0.3000 = -91639.5349 -Energy at 0.4000 = -91639.3275 -Energy at 0.5000 = -91639.0354 -Energy at 0.6000 = -91638.6206 -Energy at 0.7000 = -91638.0098 -Energy at 0.8000 = -91637.0570 -Energy at 0.9000 = -91635.4407 -Energy at 1.0000 = -91632.3353 +Energy at 0.0000 = -91639.6756 +Energy at 0.1000 = -91639.6376 +Energy at 0.2000 = -91639.5271 +Energy at 0.3000 = -91639.3552 +Energy at 0.4000 = -91639.1174 +Energy at 0.5000 = -91638.7954 +Energy at 0.6000 = -91638.3511 +Energy at 0.7000 = -91637.7116 +Energy at 0.8000 = -91636.7317 +Energy at 0.9000 = -91635.0914 +Energy at 1.0000 = -91631.9712 ------------------------------------------------------------------------------ @@ -474,22 +497,22 @@ Energy at 1.0000 = -91632.3353 NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 304.93 PRESS = 0.0 - Etot = -73137.7161 EKtot = 18500.9045 EPtot = -91638.6206 - BOND = 478.4966 ANGLE = 1214.5510 DIHED = 1748.4541 - 1-4 NB = 608.2822 1-4 EEL = 6275.9002 VDWAALS = 11276.7498 - EELEC = -113241.0545 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73137.3956 EKtot = 18500.9555 EPtot = -91638.3511 + BOND = 478.5985 ANGLE = 1214.5172 DIHED = 1748.4545 + 1-4 NB = 608.4927 1-4 EEL = 6275.8909 VDWAALS = 11276.7478 + EELEC = -113241.0526 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0110 - DV/DL = 4.9642 + DV/DL = 5.2557 ------------------------------------------------------------------------------ - Softcore part of the system: 1 atoms, TEMP(K) = 364.30 - SC_Etot= 2.1882 SC_EKtot= 1.0859 SC_EPtot = 1.1023 - SC_BOND= 0.8125 SC_ANGLE= 0.2328 SC_DIHED = 0.0397 - SC_14NB= 0.0172 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 1 atoms, TEMP(K) = 363.11 + SC_Etot= 2.1771 SC_EKtot= 1.0824 SC_EPtot = 1.0948 + SC_BOND= 0.8083 SC_ANGLE= 0.2465 SC_DIHED = 0.0400 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.5497 SC_DERIV = 2.5497 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.5412 SC_DERIV = 2.5412 ------------------------------------------------------------------------------ @@ -497,22 +520,22 @@ Energy at 1.0000 = -91632.3353 NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 304.91 PRESS = 0.0 - Etot = -73138.4175 EKtot = 18500.2031 EPtot = -91638.6206 - BOND = 478.4966 ANGLE = 1214.5510 DIHED = 1748.4541 - 1-4 NB = 608.2822 1-4 EEL = 6275.9002 VDWAALS = 11276.7498 - EELEC = -113241.0545 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73138.0874 EKtot = 18500.2637 EPtot = -91638.3511 + BOND = 478.5985 ANGLE = 1214.5172 DIHED = 1748.4545 + 1-4 NB = 608.4927 1-4 EEL = 6275.8909 VDWAALS = 11276.7478 + EELEC = -113241.0526 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0111 - DV/DL = 4.9642 + DV/DL = 5.2557 ------------------------------------------------------------------------------ - Softcore part of the system: 2 atoms, TEMP(K) = 77.39 - SC_Etot= 1.7443 SC_EKtot= 0.3845 SC_EPtot = 1.3598 - SC_BOND= 0.0011 SC_ANGLE= 0.7501 SC_DIHED = 0.3014 - SC_14NB= 0.3073 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 2 atoms, TEMP(K) = 78.62 + SC_Etot= 1.4499 SC_EKtot= 0.3906 SC_EPtot = 1.0593 + SC_BOND= 0.0021 SC_ANGLE= 0.7557 SC_DIHED = 0.3015 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.5497 SC_DERIV = 2.5497 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.5412 SC_DERIV = 2.5412 ------------------------------------------------------------------------------ @@ -523,22 +546,22 @@ Energy at 1.0000 = -91632.3353 NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 301.95 PRESS = 0.0 - Etot = -73135.4719 EKtot = 18320.4093 EPtot = -91455.8812 - BOND = 481.6195 ANGLE = 1235.6667 DIHED = 1759.5665 - 1-4 NB = 610.3718 1-4 EEL = 6272.4707 VDWAALS = 11248.2670 - EELEC = -113063.8434 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73135.3625 EKtot = 18320.4363 EPtot = -91455.7988 + BOND = 481.6466 ANGLE = 1235.6530 DIHED = 1759.5668 + 1-4 NB = 610.4448 1-4 EEL = 6272.4642 VDWAALS = 11248.2681 + EELEC = -113063.8422 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0110 - DV/DL = 5.5023 + DV/DL = 5.6191 ------------------------------------------------------------------------------ - Softcore part of the system: 1 atoms, TEMP(K) = 407.11 - SC_Etot= 2.4879 SC_EKtot= 1.2135 SC_EPtot = 1.2744 - SC_BOND= 0.4591 SC_ANGLE= 0.1246 SC_DIHED = 0.6969 - SC_14NB= -0.0063 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 1 atoms, TEMP(K) = 406.98 + SC_Etot= 2.5006 SC_EKtot= 1.2131 SC_EPtot = 1.2875 + SC_BOND= 0.4608 SC_ANGLE= 0.1293 SC_DIHED = 0.6974 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6622 SC_DERIV = 2.6622 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6588 SC_DERIV = 2.6588 ------------------------------------------------------------------------------ @@ -546,22 +569,22 @@ Energy at 1.0000 = -91632.3353 NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 3.00 PRESS = 0.0 - Etot = 2.1445 EKtot = 181.8314 EPtot = 183.9548 - BOND = 16.5570 ANGLE = 47.8689 DIHED = 12.3665 - 1-4 NB = 1.5073 1-4 EEL = 7.9590 VDWAALS = 23.9856 - EELEC = 178.5900 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = 2.0265 EKtot = 181.8521 EPtot = 183.8524 + BOND = 16.5545 ANGLE = 47.8871 DIHED = 12.3656 + 1-4 NB = 1.4622 1-4 EEL = 7.9564 VDWAALS = 23.9838 + EELEC = 178.5895 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 0.0039 Density = 0.0000 - DV/DL = 0.4640 + DV/DL = 0.4439 ------------------------------------------------------------------------------ - Softcore part of the system: 1 atoms, TEMP(K) = 159.58 - SC_Etot= 0.3123 SC_EKtot= 0.4757 SC_EPtot = 0.7093 - SC_BOND= 0.3122 SC_ANGLE= 0.0629 SC_DIHED = 0.5897 - SC_14NB= 0.0187 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 1 atoms, TEMP(K) = 159.45 + SC_Etot= 0.3188 SC_EKtot= 0.4753 SC_EPtot = 0.7054 + SC_BOND= 0.3124 SC_ANGLE= 0.0680 SC_DIHED = 0.5903 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0853 SC_DERIV = 0.0853 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0868 SC_DERIV = 0.0868 ------------------------------------------------------------------------------ @@ -572,22 +595,22 @@ Energy at 1.0000 = -91632.3353 NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 301.93 PRESS = 0.0 - Etot = -73136.3168 EKtot = 18319.5644 EPtot = -91455.8812 - BOND = 481.6195 ANGLE = 1235.6667 DIHED = 1759.5665 - 1-4 NB = 610.3718 1-4 EEL = 6272.4707 VDWAALS = 11248.2670 - EELEC = -113063.8434 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73136.2005 EKtot = 18319.5983 EPtot = -91455.7988 + BOND = 481.6466 ANGLE = 1235.6530 DIHED = 1759.5668 + 1-4 NB = 610.4448 1-4 EEL = 6272.4642 VDWAALS = 11248.2681 + EELEC = -113063.8422 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0111 - DV/DL = 5.5023 + DV/DL = 5.6191 ------------------------------------------------------------------------------ - Softcore part of the system: 2 atoms, TEMP(K) = 74.20 - SC_Etot= 1.6275 SC_EKtot= 0.3686 SC_EPtot = 1.2589 - SC_BOND= 0.0145 SC_ANGLE= 0.5363 SC_DIHED = 0.5973 - SC_14NB= 0.1108 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 2 atoms, TEMP(K) = 75.51 + SC_Etot= 1.5245 SC_EKtot= 0.3751 SC_EPtot = 1.1494 + SC_BOND= 0.0151 SC_ANGLE= 0.5373 SC_DIHED = 0.5970 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6622 SC_DERIV = 2.6622 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6588 SC_DERIV = 2.6588 ------------------------------------------------------------------------------ @@ -595,22 +618,22 @@ Energy at 1.0000 = -91632.3353 NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 3.00 PRESS = 0.0 - Etot = 1.8791 EKtot = 182.1373 EPtot = 183.9548 - BOND = 16.5570 ANGLE = 47.8689 DIHED = 12.3665 - 1-4 NB = 1.5073 1-4 EEL = 7.9590 VDWAALS = 23.9856 - EELEC = 178.5900 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = 1.7616 EKtot = 182.1600 EPtot = 183.8524 + BOND = 16.5545 ANGLE = 47.8871 DIHED = 12.3656 + 1-4 NB = 1.4622 1-4 EEL = 7.9564 VDWAALS = 23.9838 + EELEC = 178.5895 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 0.0039 Density = 0.0000 - DV/DL = 0.4640 + DV/DL = 0.4439 ------------------------------------------------------------------------------ - Softcore part of the system: 2 atoms, TEMP(K) = 25.31 - SC_Etot= 0.1455 SC_EKtot= 0.1257 SC_EPtot = 0.1759 - SC_BOND= 0.0183 SC_ANGLE= 0.1455 SC_DIHED = 0.2073 - SC_14NB= 0.1329 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 2 atoms, TEMP(K) = 24.90 + SC_Etot= 0.1480 SC_EKtot= 0.1237 SC_EPtot = 0.1311 + SC_BOND= 0.0183 SC_ANGLE= 0.1477 SC_DIHED = 0.2070 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0853 SC_DERIV = 0.0853 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0868 SC_DERIV = 0.0868 ------------------------------------------------------------------------------ @@ -618,13 +641,13 @@ Energy at 1.0000 = -91632.3353 NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 3.00 PRESS = 0.0 - Etot = 0.0000 EKtot = 0.0000 EPtot = 2.7694 + Etot = 0.0000 EKtot = 0.0000 EPtot = 2.8026 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 - 1-4 NB = 0.0000 1-4 EEL = -8.1252 VDWAALS = -1.5836 - EELEC = 12.5489 EHBOND = 0.0000 RESTRAINT = 0.0000 + 1-4 NB = 0.1246 1-4 EEL = -8.1289 VDWAALS = -1.5853 + EELEC = 12.5499 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 0.0000 Density = 0.0000 - DV/DL = 2.7694 + DV/DL = 2.8026 ------------------------------------------------------------------------------ | MC Barostat: 2 volume changes attempted. @@ -639,15 +662,15 @@ Energy at 1.0000 = -91632.3353 | | Routine Sec % | ------------------------------ -| Nonbond 0.01 5.26 +| Nonbond 0.01 8.09 | Bond 0.00 0.00 | Angle 0.00 0.00 | Dihedral 0.00 0.00 -| Shake 0.00 0.00 -| RunMD 0.14 89.47 -| Other 0.01 5.26 +| Shake 0.00 0.09 +| RunMD 0.11 90.16 +| Other 0.00 1.65 | ------------------------------ -| Total 0.15 +| Total 0.12 | PME Nonbond Pairlist CPU Time: | @@ -664,9 +687,9 @@ Energy at 1.0000 = -91632.3353 | --------------------------------- | NonBonded Calc 0.00 0.00 | Exclude Masked 0.00 0.00 -| Other 0.00 0.00 +| Other 0.00 0.03 | --------------------------------- -| Total 0.00 0.00 +| Total 0.00 0.03 | PME Reciprocal Force CPU Time: | @@ -683,17 +706,17 @@ Energy at 1.0000 = -91632.3353 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 15 steps: -| Elapsed(s) = 0.14 Per Step(ms) = 9.01 -| ns/day = 9.58 seconds/ns = 9014.93 +| Elapsed(s) = 0.11 Per Step(ms) = 7.26 +| ns/day = 11.90 seconds/ns = 7262.00 | | Average timings for all steps: -| Elapsed(s) = 0.15 Per Step(ms) = 7.49 -| ns/day = 11.53 seconds/ns = 7491.04 +| Elapsed(s) = 0.12 Per Step(ms) = 5.84 +| ns/day = 14.80 seconds/ns = 5836.85 | ----------------------------------------------------- -| Setup CPU time: 0.98 seconds -| NonSetup CPU time: 0.15 seconds -| Total CPU time: 1.14 seconds 0.00 hours +| Setup CPU time: 0.48 seconds +| NonSetup CPU time: 0.12 seconds +| Total CPU time: 0.60 seconds 0.00 hours | Setup wall time: 1 seconds | NonSetup wall time: 0 seconds diff --git test/cuda/gti/AFE_MBAR/softcore/complex/complex.out.SPFP test/cuda/gti/AFE_MBAR/softcore/complex/complex.out.SPFP index 12714fcd96..787b2a2b14 100644 --- test/cuda/gti/AFE_MBAR/softcore/complex/complex.out.SPFP +++ test/cuda/gti/AFE_MBAR/softcore/complex/complex.out.SPFP @@ -1,14 +1,14 @@ ------------------------------------------------------- - Amber 16 PMEMD 2016 + Amber 18 PMEMD 2018 ------------------------------------------------------- -| PMEMD implementation of SANDER, Release 16 +| PMEMD implementation of SANDER, Release 18 -| Run on 04/11/2018 at 12:05:55 +| Run on 08/12/2019 at 14:15:03 -| Executable path: /home/cruzeiro/amber/bin/pmemd.cuda_SPFP -| Working directory: /home/cruzeiro/amber/test/cuda/gti/AFE_MBAR/softcore/complex +| Executable path: /usr/people/taisung/amber/amber_release/bin/pmemd.cuda_SPFP +| Working directory: /usr/people/taisung/amber/amber_release/test/cuda/gti/AFE_MBAR/softcore/complex | Hostname: Unknown [-O]verwriting output @@ -126,13 +126,13 @@ NPT test |------------------- GPU DEVICE INFO -------------------- | -| CUDA_VISIBLE_DEVICES: not set -| CUDA Capable Devices Detected: 3 -| CUDA Device ID in use: 1 -| CUDA Device Name: GeForce GTX 1080 Ti -| CUDA Device Global Mem Size: 11172 MB -| CUDA Device Num Multiprocessors: 28 -| CUDA Device Core Freq: 1.58 GHz +| CUDA_VISIBLE_DEVICES: 0,1 +| CUDA Capable Devices Detected: 2 +| CUDA Device ID in use: 0 +| CUDA Device Name: TITAN V +| CUDA Device Global Mem Size: 12066 MB +| CUDA Device Num Multiprocessors: 80 +| CUDA Device Core Freq: 1.46 GHz | |-------------------------------------------------------- @@ -302,17 +302,17 @@ Total charge of -0.04433900 removed from 3 atoms SHAKE constraints in the SC region: 1 MBAR Energy analysis: -Energy at 0.0000 = -91164.9862 -Energy at 0.1000 = -91165.0009 -Energy at 0.2000 = -91164.9311 -Energy at 0.3000 = -91164.7922 -Energy at 0.4000 = -91164.5819 -Energy at 0.5000 = -91164.2821 -Energy at 0.6000 = -91163.8544 -Energy at 0.7000 = -91163.2255 -Energy at 0.8000 = -91162.2498 -Energy at 0.9000 = -91160.6105 -Energy at 1.0000 = -91157.5043 +Energy at 0.0000 = -91165.0016 +Energy at 0.1000 = -91165.0179 +Energy at 0.2000 = -91164.9497 +Energy at 0.3000 = -91164.8123 +Energy at 0.4000 = -91164.6035 +Energy at 0.5000 = -91164.3052 +Energy at 0.6000 = -91163.8791 +Energy at 0.7000 = -91163.2516 +Energy at 0.8000 = -91162.2775 +Energy at 0.9000 = -91160.6397 +Energy at 1.0000 = -91157.5351 ------------------------------------------------------------------------------ @@ -320,22 +320,22 @@ Energy at 1.0000 = -91157.5043 NSTEP = 5 TIME(PS) = 250.005 TEMP(K) = 297.20 PRESS = 0.0 - Etot = -73131.9074 EKtot = 18031.9470 EPtot = -91163.8544 - BOND = 508.4395 ANGLE = 1292.6930 DIHED = 1775.5206 - 1-4 NB = 611.4277 1-4 EEL = 6260.5476 VDWAALS = 11214.7283 - EELEC = -112827.2110 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73131.9464 EKtot = 18031.9327 EPtot = -91163.8791 + BOND = 508.4360 ANGLE = 1292.6994 DIHED = 1775.5199 + 1-4 NB = 611.3997 1-4 EEL = 6260.5456 VDWAALS = 11214.7309 + EELEC = -112827.2106 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0110 - DV/DL = 5.1188 + DV/DL = 5.1037 ------------------------------------------------------------------------------ - Softcore part of the system: 1 atoms, TEMP(K) = 613.51 - SC_Etot= 2.1681 SC_EKtot= 1.8287 SC_EPtot = 0.3394 - SC_BOND= 0.0000 SC_ANGLE= 0.0858 SC_DIHED = 0.2740 - SC_14NB= -0.0204 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 1 atoms, TEMP(K) = 613.46 + SC_Etot= 2.1892 SC_EKtot= 1.8286 SC_EPtot = 0.3606 + SC_BOND= 0.0000 SC_ANGLE= 0.0871 SC_DIHED = 0.2735 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6367 SC_DERIV = 2.6367 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6364 SC_DERIV = 2.6364 ------------------------------------------------------------------------------ @@ -343,37 +343,37 @@ Energy at 1.0000 = -91157.5043 NSTEP = 5 TIME(PS) = 250.005 TEMP(K) = 297.17 PRESS = 0.0 - Etot = -73133.2020 EKtot = 18030.6525 EPtot = -91163.8544 - BOND = 508.4395 ANGLE = 1292.6930 DIHED = 1775.5206 - 1-4 NB = 611.4277 1-4 EEL = 6260.5476 VDWAALS = 11214.7283 - EELEC = -112827.2110 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73133.2375 EKtot = 18030.6416 EPtot = -91163.8791 + BOND = 508.4360 ANGLE = 1292.6994 DIHED = 1775.5199 + 1-4 NB = 611.3997 1-4 EEL = 6260.5456 VDWAALS = 11214.7309 + EELEC = -112827.2106 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0111 - DV/DL = 5.1188 + DV/DL = 5.1037 ------------------------------------------------------------------------------ - Softcore part of the system: 2 atoms, TEMP(K) = 107.53 - SC_Etot= 1.7294 SC_EKtot= 0.5342 SC_EPtot = 1.1952 - SC_BOND= 0.0051 SC_ANGLE= 0.3800 SC_DIHED = 0.8451 - SC_14NB= -0.0350 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 2 atoms, TEMP(K) = 108.19 + SC_Etot= 1.7672 SC_EKtot= 0.5375 SC_EPtot = 1.2297 + SC_BOND= 0.0050 SC_ANGLE= 0.3801 SC_DIHED = 0.8446 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6367 SC_DERIV = 2.6367 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6364 SC_DERIV = 2.6364 ------------------------------------------------------------------------------ MBAR Energy analysis: -Energy at 0.0000 = -91438.4153 -Energy at 0.1000 = -91438.4762 -Energy at 0.2000 = -91438.3896 -Energy at 0.3000 = -91438.2046 -Energy at 0.4000 = -91437.9328 -Energy at 0.5000 = -91437.5621 -Energy at 0.6000 = -91437.0550 -Energy at 0.7000 = -91436.3329 -Energy at 0.8000 = -91435.2337 -Energy at 0.9000 = -91433.3884 -Energy at 1.0000 = -91429.8128 +Energy at 0.0000 = -91438.4954 +Energy at 0.1000 = -91438.5530 +Energy at 0.2000 = -91438.4625 +Energy at 0.3000 = -91438.2733 +Energy at 0.4000 = -91437.9973 +Energy at 0.5000 = -91437.6222 +Energy at 0.6000 = -91437.1107 +Energy at 0.7000 = -91436.3844 +Energy at 0.8000 = -91435.2811 +Energy at 0.9000 = -91433.4319 +Energy at 1.0000 = -91429.8533 ------------------------------------------------------------------------------ @@ -381,83 +381,83 @@ Energy at 1.0000 = -91429.8128 NSTEP = 10 TIME(PS) = 250.010 TEMP(K) = 301.64 PRESS = 0.0 - Etot = -73135.5711 EKtot = 18301.4839 EPtot = -91437.0550 - BOND = 463.1871 ANGLE = 1168.6040 DIHED = 1767.6822 - 1-4 NB = 609.6493 1-4 EEL = 6271.0879 VDWAALS = 11237.4963 - EELEC = -112954.7617 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73135.5792 EKtot = 18301.5315 EPtot = -91437.1107 + BOND = 463.1644 ANGLE = 1168.5709 DIHED = 1767.6815 + 1-4 NB = 609.6525 1-4 EEL = 6271.0817 VDWAALS = 11237.4994 + EELEC = -112954.7610 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0110 - DV/DL = 5.9672 + DV/DL = 6.0102 ------------------------------------------------------------------------------ - Softcore part of the system: 1 atoms, TEMP(K) = 473.73 - SC_Etot= 2.7419 SC_EKtot= 1.4121 SC_EPtot = 1.3298 - SC_BOND= 0.3561 SC_ANGLE= 0.0793 SC_DIHED = 0.9227 - SC_14NB= -0.0283 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 1 atoms, TEMP(K) = 473.87 + SC_Etot= 2.7762 SC_EKtot= 1.4125 SC_EPtot = 1.3637 + SC_BOND= 0.3577 SC_ANGLE= 0.0822 SC_DIHED = 0.9238 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6753 SC_DERIV = 2.6753 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6740 SC_DERIV = 2.6740 ------------------------------------------------------------------------------ | TI region 2 - NSTEP = 10 TIME(PS) = 250.010 TEMP(K) = 301.61 PRESS = 0.0 - Etot = -73136.6075 EKtot = 18300.4475 EPtot = -91437.0550 - BOND = 463.1871 ANGLE = 1168.6040 DIHED = 1767.6822 - 1-4 NB = 609.6493 1-4 EEL = 6271.0879 VDWAALS = 11237.4963 - EELEC = -112954.7617 EHBOND = 0.0000 RESTRAINT = 0.0000 + NSTEP = 10 TIME(PS) = 250.010 TEMP(K) = 301.62 PRESS = 0.0 + Etot = -73136.6085 EKtot = 18300.5022 EPtot = -91437.1107 + BOND = 463.1644 ANGLE = 1168.5709 DIHED = 1767.6815 + 1-4 NB = 609.6525 1-4 EEL = 6271.0817 VDWAALS = 11237.4994 + EELEC = -112954.7610 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0111 - DV/DL = 5.9672 + DV/DL = 6.0102 ------------------------------------------------------------------------------ - Softcore part of the system: 2 atoms, TEMP(K) = 75.62 - SC_Etot= 1.3827 SC_EKtot= 0.3757 SC_EPtot = 1.0070 - SC_BOND= 0.0460 SC_ANGLE= 0.4271 SC_DIHED = 0.5172 - SC_14NB= 0.0167 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 2 atoms, TEMP(K) = 77.14 + SC_Etot= 1.3730 SC_EKtot= 0.3832 SC_EPtot = 0.9898 + SC_BOND= 0.0466 SC_ANGLE= 0.4264 SC_DIHED = 0.5168 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6753 SC_DERIV = 2.6753 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6740 SC_DERIV = 2.6740 ------------------------------------------------------------------------------ MBAR Energy analysis: -Energy at 0.0000 = -91585.2812 -Energy at 0.1000 = -91585.2462 -Energy at 0.2000 = -91585.1185 -Energy at 0.3000 = -91584.9178 -Energy at 0.4000 = -91584.6430 -Energy at 0.5000 = -91584.2748 -Energy at 0.6000 = -91583.7703 -Energy at 0.7000 = -91583.0439 -Energy at 0.8000 = -91581.9175 -Energy at 0.9000 = -91579.9779 -Energy at 1.0000 = -91576.0877 +Energy at 0.0000 = -91585.2334 +Energy at 0.1000 = -91585.1826 +Energy at 0.2000 = -91585.0395 +Energy at 0.3000 = -91584.8234 +Energy at 0.4000 = -91584.5334 +Energy at 0.5000 = -91584.1501 +Energy at 0.6000 = -91583.6308 +Energy at 0.7000 = -91582.8898 +Energy at 0.8000 = -91581.7494 +Energy at 0.9000 = -91579.7975 +Energy at 1.0000 = -91575.8992 ------------------------------------------------------------------------------ | TI region 1 - NSTEP = 15 TIME(PS) = 250.015 TEMP(K) = 304.04 PRESS = 0.0 - Etot = -73136.4675 EKtot = 18447.3028 EPtot = -91583.7703 - BOND = 476.3550 ANGLE = 1266.8187 DIHED = 1746.6102 - 1-4 NB = 612.1279 1-4 EEL = 6282.3473 VDWAALS = 11264.0674 - EELEC = -113232.0968 EHBOND = 0.0000 RESTRAINT = 0.0000 + NSTEP = 15 TIME(PS) = 250.015 TEMP(K) = 304.05 PRESS = 0.0 + Etot = -73136.3034 EKtot = 18447.3274 EPtot = -91583.6308 + BOND = 476.3875 ANGLE = 1266.8245 DIHED = 1746.6124 + 1-4 NB = 612.2340 1-4 EEL = 6282.3388 VDWAALS = 11264.0681 + EELEC = -113232.0960 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0110 - DV/DL = 5.9590 + DV/DL = 6.1066 ------------------------------------------------------------------------------ - Softcore part of the system: 1 atoms, TEMP(K) = 176.90 - SC_Etot= 2.8532 SC_EKtot= 0.5273 SC_EPtot = 2.3259 - SC_BOND= 0.6680 SC_ANGLE= 0.1005 SC_DIHED = 1.5510 - SC_14NB= 0.0064 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 1 atoms, TEMP(K) = 177.49 + SC_Etot= 2.8599 SC_EKtot= 0.5291 SC_EPtot = 2.3308 + SC_BOND= 0.6770 SC_ANGLE= 0.1016 SC_DIHED = 1.5522 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.7872 SC_DERIV = 2.7872 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.7835 SC_DERIV = 2.7835 ------------------------------------------------------------------------------ @@ -465,37 +465,37 @@ Energy at 1.0000 = -91576.0877 NSTEP = 15 TIME(PS) = 250.015 TEMP(K) = 304.03 PRESS = 0.0 - Etot = -73136.8147 EKtot = 18446.9556 EPtot = -91583.7703 - BOND = 476.3550 ANGLE = 1266.8187 DIHED = 1746.6102 - 1-4 NB = 612.1279 1-4 EEL = 6282.3473 VDWAALS = 11264.0674 - EELEC = -113232.0968 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73136.6432 EKtot = 18446.9876 EPtot = -91583.6308 + BOND = 476.3875 ANGLE = 1266.8245 DIHED = 1746.6124 + 1-4 NB = 612.2340 1-4 EEL = 6282.3388 VDWAALS = 11264.0681 + EELEC = -113232.0960 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0111 - DV/DL = 5.9590 + DV/DL = 6.1066 ------------------------------------------------------------------------------ - Softcore part of the system: 2 atoms, TEMP(K) = 36.26 - SC_Etot= 1.6537 SC_EKtot= 0.1801 SC_EPtot = 1.4736 - SC_BOND= 0.0058 SC_ANGLE= 0.5879 SC_DIHED = 0.7255 - SC_14NB= 0.1543 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 2 atoms, TEMP(K) = 38.09 + SC_Etot= 1.5080 SC_EKtot= 0.1893 SC_EPtot = 1.3188 + SC_BOND= 0.0067 SC_ANGLE= 0.5871 SC_DIHED = 0.7249 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.7872 SC_DERIV = 2.7872 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.7835 SC_DERIV = 2.7835 ------------------------------------------------------------------------------ MBAR Energy analysis: -Energy at 0.0000 = -91639.6823 -Energy at 0.1000 = -91639.6763 -Energy at 0.2000 = -91639.5970 -Energy at 0.3000 = -91639.4556 -Energy at 0.4000 = -91639.2482 -Energy at 0.5000 = -91638.9562 -Energy at 0.6000 = -91638.5413 -Energy at 0.7000 = -91637.9305 -Energy at 0.8000 = -91636.9778 -Energy at 0.9000 = -91635.3615 -Energy at 1.0000 = -91632.2561 +Energy at 0.0000 = -91639.5958 +Energy at 0.1000 = -91639.5578 +Energy at 0.2000 = -91639.4473 +Energy at 0.3000 = -91639.2753 +Energy at 0.4000 = -91639.0376 +Energy at 0.5000 = -91638.7156 +Energy at 0.6000 = -91638.2713 +Energy at 0.7000 = -91637.6318 +Energy at 0.8000 = -91636.6518 +Energy at 0.9000 = -91635.0116 +Energy at 1.0000 = -91631.8913 ------------------------------------------------------------------------------ @@ -503,22 +503,22 @@ Energy at 1.0000 = -91632.2561 NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 304.93 PRESS = 0.0 - Etot = -73137.6379 EKtot = 18500.9034 EPtot = -91638.5413 - BOND = 478.4966 ANGLE = 1214.5510 DIHED = 1748.4545 - 1-4 NB = 608.2821 1-4 EEL = 6275.9004 VDWAALS = 11276.7430 - EELEC = -113240.9689 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73137.3139 EKtot = 18500.9574 EPtot = -91638.2713 + BOND = 478.5985 ANGLE = 1214.5170 DIHED = 1748.4551 + 1-4 NB = 608.4927 1-4 EEL = 6275.8911 VDWAALS = 11276.7408 + EELEC = -113240.9664 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0110 - DV/DL = 4.9642 + DV/DL = 5.2557 ------------------------------------------------------------------------------ - Softcore part of the system: 1 atoms, TEMP(K) = 364.31 - SC_Etot= 2.1882 SC_EKtot= 1.0859 SC_EPtot = 1.1023 - SC_BOND= 0.8125 SC_ANGLE= 0.2328 SC_DIHED = 0.0397 - SC_14NB= 0.0172 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 1 atoms, TEMP(K) = 363.11 + SC_Etot= 2.1771 SC_EKtot= 1.0824 SC_EPtot = 1.0948 + SC_BOND= 0.8083 SC_ANGLE= 0.2465 SC_DIHED = 0.0400 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.5497 SC_DERIV = 2.5497 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.5412 SC_DERIV = 2.5412 ------------------------------------------------------------------------------ @@ -526,22 +526,22 @@ Energy at 1.0000 = -91632.2561 NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 304.91 PRESS = 0.0 - Etot = -73138.3393 EKtot = 18500.2020 EPtot = -91638.5413 - BOND = 478.4966 ANGLE = 1214.5510 DIHED = 1748.4545 - 1-4 NB = 608.2821 1-4 EEL = 6275.9004 VDWAALS = 11276.7430 - EELEC = -113240.9689 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73138.0057 EKtot = 18500.2656 EPtot = -91638.2713 + BOND = 478.5985 ANGLE = 1214.5170 DIHED = 1748.4551 + 1-4 NB = 608.4927 1-4 EEL = 6275.8911 VDWAALS = 11276.7408 + EELEC = -113240.9664 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0111 - DV/DL = 4.9642 + DV/DL = 5.2557 ------------------------------------------------------------------------------ - Softcore part of the system: 2 atoms, TEMP(K) = 77.39 - SC_Etot= 1.7443 SC_EKtot= 0.3845 SC_EPtot = 1.3598 - SC_BOND= 0.0011 SC_ANGLE= 0.7501 SC_DIHED = 0.3014 - SC_14NB= 0.3073 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 2 atoms, TEMP(K) = 78.62 + SC_Etot= 1.4499 SC_EKtot= 0.3906 SC_EPtot = 1.0593 + SC_BOND= 0.0021 SC_ANGLE= 0.7557 SC_DIHED = 0.3015 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.5497 SC_DERIV = 2.5497 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.5412 SC_DERIV = 2.5412 ------------------------------------------------------------------------------ @@ -552,22 +552,22 @@ Energy at 1.0000 = -91632.2561 NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 301.95 PRESS = 0.0 - Etot = -73135.3960 EKtot = 18320.4093 EPtot = -91455.8053 - BOND = 481.6195 ANGLE = 1235.6667 DIHED = 1759.5669 - 1-4 NB = 610.3717 1-4 EEL = 6272.4708 VDWAALS = 11248.2587 - EELEC = -113063.7596 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73135.2857 EKtot = 18320.4372 EPtot = -91455.7230 + BOND = 481.6466 ANGLE = 1235.6529 DIHED = 1759.5672 + 1-4 NB = 610.4447 1-4 EEL = 6272.4643 VDWAALS = 11248.2598 + EELEC = -113063.7585 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0110 - DV/DL = 5.5023 + DV/DL = 5.6190 ------------------------------------------------------------------------------ - Softcore part of the system: 1 atoms, TEMP(K) = 407.11 - SC_Etot= 2.4879 SC_EKtot= 1.2135 SC_EPtot = 1.2744 - SC_BOND= 0.4591 SC_ANGLE= 0.1246 SC_DIHED = 0.6969 - SC_14NB= -0.0063 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 1 atoms, TEMP(K) = 406.98 + SC_Etot= 2.5006 SC_EKtot= 1.2131 SC_EPtot = 1.2875 + SC_BOND= 0.4608 SC_ANGLE= 0.1293 SC_DIHED = 0.6974 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6622 SC_DERIV = 2.6622 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6588 SC_DERIV = 2.6588 ------------------------------------------------------------------------------ @@ -575,22 +575,22 @@ Energy at 1.0000 = -91632.2561 NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 3.00 PRESS = 0.0 - Etot = 2.1433 EKtot = 181.8301 EPtot = 183.9527 - BOND = 16.5570 ANGLE = 47.8689 DIHED = 12.3667 - 1-4 NB = 1.5073 1-4 EEL = 7.9590 VDWAALS = 23.9864 - EELEC = 178.5892 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = 2.0240 EKtot = 181.8522 EPtot = 183.8502 + BOND = 16.5545 ANGLE = 47.8871 DIHED = 12.3657 + 1-4 NB = 1.4622 1-4 EEL = 7.9564 VDWAALS = 23.9846 + EELEC = 178.5886 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 0.0039 Density = 0.0000 - DV/DL = 0.4640 + DV/DL = 0.4439 ------------------------------------------------------------------------------ - Softcore part of the system: 1 atoms, TEMP(K) = 159.58 - SC_Etot= 0.3123 SC_EKtot= 0.4757 SC_EPtot = 0.7093 - SC_BOND= 0.3122 SC_ANGLE= 0.0629 SC_DIHED = 0.5897 - SC_14NB= 0.0187 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 1 atoms, TEMP(K) = 159.45 + SC_Etot= 0.3188 SC_EKtot= 0.4753 SC_EPtot = 0.7054 + SC_BOND= 0.3124 SC_ANGLE= 0.0680 SC_DIHED = 0.5903 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0853 SC_DERIV = 0.0853 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0868 SC_DERIV = 0.0868 ------------------------------------------------------------------------------ @@ -601,22 +601,22 @@ Energy at 1.0000 = -91632.2561 NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 301.93 PRESS = 0.0 - Etot = -73136.2409 EKtot = 18319.5644 EPtot = -91455.8053 - BOND = 481.6195 ANGLE = 1235.6667 DIHED = 1759.5669 - 1-4 NB = 610.3717 1-4 EEL = 6272.4708 VDWAALS = 11248.2587 - EELEC = -113063.7596 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73136.1237 EKtot = 18319.5992 EPtot = -91455.7230 + BOND = 481.6466 ANGLE = 1235.6529 DIHED = 1759.5672 + 1-4 NB = 610.4447 1-4 EEL = 6272.4643 VDWAALS = 11248.2598 + EELEC = -113063.7585 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0111 - DV/DL = 5.5023 + DV/DL = 5.6190 ------------------------------------------------------------------------------ - Softcore part of the system: 2 atoms, TEMP(K) = 74.20 - SC_Etot= 1.6275 SC_EKtot= 0.3686 SC_EPtot = 1.2589 - SC_BOND= 0.0145 SC_ANGLE= 0.5363 SC_DIHED = 0.5973 - SC_14NB= 0.1108 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 2 atoms, TEMP(K) = 75.51 + SC_Etot= 1.5245 SC_EKtot= 0.3751 SC_EPtot = 1.1494 + SC_BOND= 0.0151 SC_ANGLE= 0.5373 SC_DIHED = 0.5970 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6622 SC_DERIV = 2.6622 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6588 SC_DERIV = 2.6588 ------------------------------------------------------------------------------ @@ -624,22 +624,22 @@ Energy at 1.0000 = -91632.2561 NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 3.00 PRESS = 0.0 - Etot = 1.8776 EKtot = 182.1360 EPtot = 183.9527 - BOND = 16.5570 ANGLE = 47.8689 DIHED = 12.3667 - 1-4 NB = 1.5073 1-4 EEL = 7.9590 VDWAALS = 23.9864 - EELEC = 178.5892 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = 1.7591 EKtot = 182.1602 EPtot = 183.8502 + BOND = 16.5545 ANGLE = 47.8871 DIHED = 12.3657 + 1-4 NB = 1.4622 1-4 EEL = 7.9564 VDWAALS = 23.9846 + EELEC = 178.5886 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 0.0039 Density = 0.0000 - DV/DL = 0.4640 + DV/DL = 0.4439 ------------------------------------------------------------------------------ - Softcore part of the system: 2 atoms, TEMP(K) = 25.31 - SC_Etot= 0.1455 SC_EKtot= 0.1257 SC_EPtot = 0.1759 - SC_BOND= 0.0183 SC_ANGLE= 0.1455 SC_DIHED = 0.2073 - SC_14NB= 0.1329 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 2 atoms, TEMP(K) = 24.90 + SC_Etot= 0.1480 SC_EKtot= 0.1237 SC_EPtot = 0.1311 + SC_BOND= 0.0183 SC_ANGLE= 0.1477 SC_DIHED = 0.2070 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0853 SC_DERIV = 0.0853 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0868 SC_DERIV = 0.0868 ------------------------------------------------------------------------------ @@ -647,13 +647,13 @@ Energy at 1.0000 = -91632.2561 NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 3.00 PRESS = 0.0 - Etot = 0.0000 EKtot = 0.0000 EPtot = 2.7695 + Etot = 0.0000 EKtot = 0.0000 EPtot = 2.8026 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 - 1-4 NB = 0.0000 1-4 EEL = -8.1252 VDWAALS = -1.5836 - EELEC = 12.5489 EHBOND = 0.0000 RESTRAINT = 0.0000 + 1-4 NB = 0.1246 1-4 EEL = -8.1289 VDWAALS = -1.5853 + EELEC = 12.5498 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 0.0000 Density = 0.0000 - DV/DL = 2.7695 + DV/DL = 2.8026 ------------------------------------------------------------------------------ | MC Barostat: 2 volume changes attempted. @@ -668,15 +668,15 @@ Energy at 1.0000 = -91632.2561 | | Routine Sec % | ------------------------------ -| Nonbond 0.01 7.50 +| Nonbond 0.01 5.77 | Bond 0.00 0.00 | Angle 0.00 0.00 | Dihedral 0.00 0.00 -| Shake 0.00 0.00 -| RunMD 0.15 92.50 -| Other 0.00 0.00 +| Shake 0.00 0.10 +| RunMD 0.10 92.29 +| Other 0.00 1.84 | ------------------------------ -| Total 0.16 +| Total 0.10 | PME Nonbond Pairlist CPU Time: | @@ -693,9 +693,9 @@ Energy at 1.0000 = -91632.2561 | --------------------------------- | NonBonded Calc 0.00 0.00 | Exclude Masked 0.00 0.00 -| Other 0.00 0.00 +| Other 0.00 0.03 | --------------------------------- -| Total 0.00 0.00 +| Total 0.00 0.03 | PME Reciprocal Force CPU Time: | @@ -712,18 +712,18 @@ Energy at 1.0000 = -91632.2561 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 15 steps: -| Elapsed(s) = 0.14 Per Step(ms) = 9.64 -| ns/day = 8.96 seconds/ns = 9638.46 +| Elapsed(s) = 0.10 Per Step(ms) = 6.60 +| ns/day = 13.08 seconds/ns = 6603.68 | | Average timings for all steps: -| Elapsed(s) = 0.16 Per Step(ms) = 7.92 -| ns/day = 10.91 seconds/ns = 7917.70 +| Elapsed(s) = 0.10 Per Step(ms) = 5.20 +| ns/day = 16.63 seconds/ns = 5196.35 | ----------------------------------------------------- -| Setup CPU time: 1.24 seconds -| NonSetup CPU time: 0.16 seconds -| Total CPU time: 1.40 seconds 0.00 hours +| Setup CPU time: 0.50 seconds +| NonSetup CPU time: 0.10 seconds +| Total CPU time: 0.61 seconds 0.00 hours -| Setup wall time: 2 seconds +| Setup wall time: 0 seconds | NonSetup wall time: 0 seconds -| Total wall time: 2 seconds 0.00 hours +| Total wall time: 0 seconds 0.00 hours diff --git test/cuda/gti/AFE_TI/softcore/complex/complex.out.DPFP test/cuda/gti/AFE_TI/softcore/complex/complex.out.DPFP index afc2a5c7fd..32ffd11e3f 100644 --- test/cuda/gti/AFE_TI/softcore/complex/complex.out.DPFP +++ test/cuda/gti/AFE_TI/softcore/complex/complex.out.DPFP @@ -1,14 +1,14 @@ ------------------------------------------------------- - Amber 16 PMEMD 2016 + Amber 18 PMEMD 2018 ------------------------------------------------------- -| PMEMD implementation of SANDER, Release 16 +| PMEMD implementation of SANDER, Release 18 -| Run on 02/13/2018 at 10:33:15 +| Run on 08/12/2019 at 14:16:57 -| Executable path: /home/taisung/amber/bin/pmemd.cuda_DPFP -| Working directory: /home/taisung/amber/test/cuda/gti/AFE_TI/softcore/complex +| Executable path: /usr/people/taisung/amber/amber_release/bin/pmemd.cuda_DPFP +| Working directory: /usr/people/taisung/amber/amber_release/test/cuda/gti/AFE_TI/softcore/complex | Hostname: Unknown [-O]verwriting output @@ -56,14 +56,17 @@ NPT test |--------------------- INFORMATION ---------------------- | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE. -| Version 16.0.0 +| Version 18.0.0 | -| 02/25/2016 +| 03/25/2018 | | Implementation by: | Ross C. Walker (SDSC) | Scott Le Grand (nVIDIA) | +| Version 18 performance extensions by: +| David Cerutti (Rutgers) +| | Precision model in use: | [DPFP] - Double Precision Forces, 64-bit Fixed point | Accumulation. @@ -89,17 +92,37 @@ NPT test | with AMBER - Part I: Generalized Born", J. Chem. | Theory Comput., 2012, 8 (5), pp1542-1555. | +| When publishing work that utilized the CUDA version +| of TI, BAR, MBAR or FEP please cite the following +| three publications in addition to the regular AMBER +| GPU citations: +| +| - Daniel J. Mermelstein; Charles Lin; Gard Nelson; +| Rachael Kretsch; J. Andrew McCammon; Ross C. Walker +| "Fast and Flexible GPU Accelerated Binding +| Free Energy Calculations within the AMBER Molecular +| Dynamics Package" J. Comp. Chem., 2018, +| DOI: 10.1002/jcc.25187 +| +| - Tai-Sung Lee; Yuan Hu; Brad Sherborne; Zhuyan Guo; +| Darrin M. York +| "Toward Fast and Accurate Binding Affinity Prediction with +| pmemdGTI: An Efficient Implementation of GPU-Accelerated +| Thermodynamic Integration" +| J. Chem. Theory Comput., 2017, 13 (7), 3077 +| +| |-------------------------------------------------------- |------------------- GPU DEVICE INFO -------------------- | -| CUDA_VISIBLE_DEVICES: not set -| CUDA Capable Devices Detected: 1 +| CUDA_VISIBLE_DEVICES: 0,1 +| CUDA Capable Devices Detected: 2 | CUDA Device ID in use: 0 -| CUDA Device Name: Tesla V100-PCIE-16GB -| CUDA Device Global Mem Size: 16152 MB +| CUDA Device Name: TITAN V +| CUDA Device Global Mem Size: 12066 MB | CUDA Device Num Multiprocessors: 80 -| CUDA Device Core Freq: 1.38 GHz +| CUDA Device Core Freq: 1.46 GHz | |-------------------------------------------------------- @@ -264,22 +287,22 @@ Total charge of -0.04433900 removed from 3 atoms NSTEP = 5 TIME(PS) = 250.005 TEMP(K) = 297.20 PRESS = 0.0 - Etot = -73131.9810 EKtot = 18031.9454 EPtot = -91163.9264 - BOND = 508.4395 ANGLE = 1292.6930 DIHED = 1775.5200 - 1-4 NB = 611.4277 1-4 EEL = 6260.5475 VDWAALS = 11214.7368 - EELEC = -112827.2910 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73132.0199 EKtot = 18031.9309 EPtot = -91163.9508 + BOND = 508.4360 ANGLE = 1292.6994 DIHED = 1775.5194 + 1-4 NB = 611.3998 1-4 EEL = 6260.5455 VDWAALS = 11214.7395 + EELEC = -112827.2904 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0110 - DV/DL = 5.1188 + DV/DL = 5.1037 ------------------------------------------------------------------------------ - Softcore part of the system: 1 atoms, TEMP(K) = 613.51 - SC_Etot= 2.1681 SC_EKtot= 1.8287 SC_EPtot = 0.3394 - SC_BOND= 0.0000 SC_ANGLE= 0.0858 SC_DIHED = 0.2740 - SC_14NB= -0.0204 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 1 atoms, TEMP(K) = 613.46 + SC_Etot= 2.1892 SC_EKtot= 1.8286 SC_EPtot = 0.3606 + SC_BOND= 0.0000 SC_ANGLE= 0.0871 SC_DIHED = 0.2735 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6367 SC_DERIV = 2.6367 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6364 SC_DERIV = 2.6364 ------------------------------------------------------------------------------ @@ -287,22 +310,22 @@ Total charge of -0.04433900 removed from 3 atoms NSTEP = 5 TIME(PS) = 250.005 TEMP(K) = 297.17 PRESS = 0.0 - Etot = -73133.2756 EKtot = 18030.6508 EPtot = -91163.9264 - BOND = 508.4395 ANGLE = 1292.6930 DIHED = 1775.5200 - 1-4 NB = 611.4277 1-4 EEL = 6260.5475 VDWAALS = 11214.7368 - EELEC = -112827.2910 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73133.3110 EKtot = 18030.6398 EPtot = -91163.9508 + BOND = 508.4360 ANGLE = 1292.6994 DIHED = 1775.5194 + 1-4 NB = 611.3998 1-4 EEL = 6260.5455 VDWAALS = 11214.7395 + EELEC = -112827.2904 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0111 - DV/DL = 5.1188 + DV/DL = 5.1037 ------------------------------------------------------------------------------ - Softcore part of the system: 2 atoms, TEMP(K) = 107.53 - SC_Etot= 1.7294 SC_EKtot= 0.5342 SC_EPtot = 1.1952 - SC_BOND= 0.0051 SC_ANGLE= 0.3800 SC_DIHED = 0.8451 - SC_14NB= -0.0350 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 2 atoms, TEMP(K) = 108.19 + SC_Etot= 1.7672 SC_EKtot= 0.5375 SC_EPtot = 1.2297 + SC_BOND= 0.0050 SC_ANGLE= 0.3801 SC_DIHED = 0.8446 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6367 SC_DERIV = 2.6367 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6364 SC_DERIV = 2.6364 ------------------------------------------------------------------------------ @@ -310,45 +333,45 @@ Total charge of -0.04433900 removed from 3 atoms NSTEP = 10 TIME(PS) = 250.010 TEMP(K) = 301.64 PRESS = 0.0 - Etot = -73135.6505 EKtot = 18301.4825 EPtot = -91437.1330 - BOND = 463.1871 ANGLE = 1168.6040 DIHED = 1767.6816 - 1-4 NB = 609.6493 1-4 EEL = 6271.0879 VDWAALS = 11237.5061 - EELEC = -112954.8491 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73135.6553 EKtot = 18301.5333 EPtot = -91437.1886 + BOND = 463.1644 ANGLE = 1168.5709 DIHED = 1767.6810 + 1-4 NB = 609.6525 1-4 EEL = 6271.0817 VDWAALS = 11237.5091 + EELEC = -112954.8481 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0110 - DV/DL = 5.9672 + DV/DL = 6.0103 ------------------------------------------------------------------------------ - Softcore part of the system: 1 atoms, TEMP(K) = 473.73 - SC_Etot= 2.7419 SC_EKtot= 1.4121 SC_EPtot = 1.3298 - SC_BOND= 0.3561 SC_ANGLE= 0.0793 SC_DIHED = 0.9227 - SC_14NB= -0.0283 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 1 atoms, TEMP(K) = 473.87 + SC_Etot= 2.7762 SC_EKtot= 1.4125 SC_EPtot = 1.3637 + SC_BOND= 0.3577 SC_ANGLE= 0.0822 SC_DIHED = 0.9238 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6753 SC_DERIV = 2.6753 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6740 SC_DERIV = 2.6740 ------------------------------------------------------------------------------ | TI region 2 - NSTEP = 10 TIME(PS) = 250.010 TEMP(K) = 301.61 PRESS = 0.0 - Etot = -73136.6869 EKtot = 18300.4461 EPtot = -91437.1330 - BOND = 463.1871 ANGLE = 1168.6040 DIHED = 1767.6816 - 1-4 NB = 609.6493 1-4 EEL = 6271.0879 VDWAALS = 11237.5061 - EELEC = -112954.8491 EHBOND = 0.0000 RESTRAINT = 0.0000 + NSTEP = 10 TIME(PS) = 250.010 TEMP(K) = 301.62 PRESS = 0.0 + Etot = -73136.6845 EKtot = 18300.5040 EPtot = -91437.1886 + BOND = 463.1644 ANGLE = 1168.5709 DIHED = 1767.6810 + 1-4 NB = 609.6525 1-4 EEL = 6271.0817 VDWAALS = 11237.5091 + EELEC = -112954.8481 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0111 - DV/DL = 5.9672 + DV/DL = 6.0103 ------------------------------------------------------------------------------ - Softcore part of the system: 2 atoms, TEMP(K) = 75.62 - SC_Etot= 1.3827 SC_EKtot= 0.3757 SC_EPtot = 1.0070 - SC_BOND= 0.0460 SC_ANGLE= 0.4271 SC_DIHED = 0.5172 - SC_14NB= 0.0167 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 2 atoms, TEMP(K) = 77.14 + SC_Etot= 1.3730 SC_EKtot= 0.3832 SC_EPtot = 0.9898 + SC_BOND= 0.0466 SC_ANGLE= 0.4264 SC_DIHED = 0.5168 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6753 SC_DERIV = 2.6753 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6740 SC_DERIV = 2.6740 ------------------------------------------------------------------------------ @@ -356,22 +379,22 @@ Total charge of -0.04433900 removed from 3 atoms NSTEP = 15 TIME(PS) = 250.015 TEMP(K) = 304.05 PRESS = 0.0 - Etot = -73136.5402 EKtot = 18447.3048 EPtot = -91583.8450 - BOND = 476.3551 ANGLE = 1266.8188 DIHED = 1746.6100 - 1-4 NB = 612.1279 1-4 EEL = 6282.3473 VDWAALS = 11264.0751 - EELEC = -113232.1791 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73136.3793 EKtot = 18447.3254 EPtot = -91583.7048 + BOND = 476.3874 ANGLE = 1266.8246 DIHED = 1746.6122 + 1-4 NB = 612.2341 1-4 EEL = 6282.3389 VDWAALS = 11264.0758 + EELEC = -113232.1778 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0110 - DV/DL = 5.9590 + DV/DL = 6.1065 ------------------------------------------------------------------------------ - Softcore part of the system: 1 atoms, TEMP(K) = 176.90 - SC_Etot= 2.8532 SC_EKtot= 0.5273 SC_EPtot = 2.3259 - SC_BOND= 0.6680 SC_ANGLE= 0.1005 SC_DIHED = 1.5510 - SC_14NB= 0.0064 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 1 atoms, TEMP(K) = 177.49 + SC_Etot= 2.8599 SC_EKtot= 0.5291 SC_EPtot = 2.3308 + SC_BOND= 0.6770 SC_ANGLE= 0.1016 SC_DIHED = 1.5522 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.7872 SC_DERIV = 2.7872 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.7835 SC_DERIV = 2.7835 ------------------------------------------------------------------------------ @@ -379,22 +402,22 @@ Total charge of -0.04433900 removed from 3 atoms NSTEP = 15 TIME(PS) = 250.015 TEMP(K) = 304.03 PRESS = 0.0 - Etot = -73136.8874 EKtot = 18446.9576 EPtot = -91583.8450 - BOND = 476.3551 ANGLE = 1266.8188 DIHED = 1746.6100 - 1-4 NB = 612.1279 1-4 EEL = 6282.3473 VDWAALS = 11264.0751 - EELEC = -113232.1791 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73136.7191 EKtot = 18446.9856 EPtot = -91583.7048 + BOND = 476.3874 ANGLE = 1266.8246 DIHED = 1746.6122 + 1-4 NB = 612.2341 1-4 EEL = 6282.3389 VDWAALS = 11264.0758 + EELEC = -113232.1778 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0111 - DV/DL = 5.9590 + DV/DL = 6.1065 ------------------------------------------------------------------------------ - Softcore part of the system: 2 atoms, TEMP(K) = 36.26 - SC_Etot= 1.6537 SC_EKtot= 0.1801 SC_EPtot = 1.4736 - SC_BOND= 0.0058 SC_ANGLE= 0.5879 SC_DIHED = 0.7255 - SC_14NB= 0.1543 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 2 atoms, TEMP(K) = 38.09 + SC_Etot= 1.5080 SC_EKtot= 0.1893 SC_EPtot = 1.3188 + SC_BOND= 0.0067 SC_ANGLE= 0.5871 SC_DIHED = 0.7249 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.7872 SC_DERIV = 2.7872 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.7835 SC_DERIV = 2.7835 ------------------------------------------------------------------------------ @@ -402,22 +425,22 @@ Total charge of -0.04433900 removed from 3 atoms NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 304.93 PRESS = 0.0 - Etot = -73137.7161 EKtot = 18500.9045 EPtot = -91638.6206 - BOND = 478.4966 ANGLE = 1214.5510 DIHED = 1748.4541 - 1-4 NB = 608.2822 1-4 EEL = 6275.9002 VDWAALS = 11276.7498 - EELEC = -113241.0545 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73137.3956 EKtot = 18500.9555 EPtot = -91638.3511 + BOND = 478.5985 ANGLE = 1214.5172 DIHED = 1748.4545 + 1-4 NB = 608.4927 1-4 EEL = 6275.8909 VDWAALS = 11276.7478 + EELEC = -113241.0526 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0110 - DV/DL = 4.9642 + DV/DL = 5.2557 ------------------------------------------------------------------------------ - Softcore part of the system: 1 atoms, TEMP(K) = 364.30 - SC_Etot= 2.1882 SC_EKtot= 1.0859 SC_EPtot = 1.1023 - SC_BOND= 0.8125 SC_ANGLE= 0.2328 SC_DIHED = 0.0397 - SC_14NB= 0.0172 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 1 atoms, TEMP(K) = 363.11 + SC_Etot= 2.1771 SC_EKtot= 1.0824 SC_EPtot = 1.0948 + SC_BOND= 0.8083 SC_ANGLE= 0.2465 SC_DIHED = 0.0400 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.5497 SC_DERIV = 2.5497 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.5412 SC_DERIV = 2.5412 ------------------------------------------------------------------------------ @@ -425,22 +448,22 @@ Total charge of -0.04433900 removed from 3 atoms NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 304.91 PRESS = 0.0 - Etot = -73138.4175 EKtot = 18500.2031 EPtot = -91638.6206 - BOND = 478.4966 ANGLE = 1214.5510 DIHED = 1748.4541 - 1-4 NB = 608.2822 1-4 EEL = 6275.9002 VDWAALS = 11276.7498 - EELEC = -113241.0545 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73138.0874 EKtot = 18500.2637 EPtot = -91638.3511 + BOND = 478.5985 ANGLE = 1214.5172 DIHED = 1748.4545 + 1-4 NB = 608.4927 1-4 EEL = 6275.8909 VDWAALS = 11276.7478 + EELEC = -113241.0526 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0111 - DV/DL = 4.9642 + DV/DL = 5.2557 ------------------------------------------------------------------------------ - Softcore part of the system: 2 atoms, TEMP(K) = 77.39 - SC_Etot= 1.7443 SC_EKtot= 0.3845 SC_EPtot = 1.3598 - SC_BOND= 0.0011 SC_ANGLE= 0.7501 SC_DIHED = 0.3014 - SC_14NB= 0.3073 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 2 atoms, TEMP(K) = 78.62 + SC_Etot= 1.4499 SC_EKtot= 0.3906 SC_EPtot = 1.0593 + SC_BOND= 0.0021 SC_ANGLE= 0.7557 SC_DIHED = 0.3015 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.5497 SC_DERIV = 2.5497 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.5412 SC_DERIV = 2.5412 ------------------------------------------------------------------------------ @@ -451,22 +474,22 @@ Total charge of -0.04433900 removed from 3 atoms NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 301.95 PRESS = 0.0 - Etot = -73135.4719 EKtot = 18320.4093 EPtot = -91455.8812 - BOND = 481.6195 ANGLE = 1235.6667 DIHED = 1759.5665 - 1-4 NB = 610.3718 1-4 EEL = 6272.4707 VDWAALS = 11248.2670 - EELEC = -113063.8434 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73135.3625 EKtot = 18320.4363 EPtot = -91455.7988 + BOND = 481.6466 ANGLE = 1235.6530 DIHED = 1759.5668 + 1-4 NB = 610.4448 1-4 EEL = 6272.4642 VDWAALS = 11248.2681 + EELEC = -113063.8422 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0110 - DV/DL = 5.5023 + DV/DL = 5.6191 ------------------------------------------------------------------------------ - Softcore part of the system: 1 atoms, TEMP(K) = 407.11 - SC_Etot= 2.4879 SC_EKtot= 1.2135 SC_EPtot = 1.2744 - SC_BOND= 0.4591 SC_ANGLE= 0.1246 SC_DIHED = 0.6969 - SC_14NB= -0.0063 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 1 atoms, TEMP(K) = 406.98 + SC_Etot= 2.5006 SC_EKtot= 1.2131 SC_EPtot = 1.2875 + SC_BOND= 0.4608 SC_ANGLE= 0.1293 SC_DIHED = 0.6974 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6622 SC_DERIV = 2.6622 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6588 SC_DERIV = 2.6588 ------------------------------------------------------------------------------ @@ -474,22 +497,22 @@ Total charge of -0.04433900 removed from 3 atoms NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 3.00 PRESS = 0.0 - Etot = 2.1445 EKtot = 181.8314 EPtot = 183.9548 - BOND = 16.5570 ANGLE = 47.8689 DIHED = 12.3665 - 1-4 NB = 1.5073 1-4 EEL = 7.9590 VDWAALS = 23.9856 - EELEC = 178.5900 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = 2.0265 EKtot = 181.8521 EPtot = 183.8524 + BOND = 16.5545 ANGLE = 47.8871 DIHED = 12.3656 + 1-4 NB = 1.4622 1-4 EEL = 7.9564 VDWAALS = 23.9838 + EELEC = 178.5895 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 0.0039 Density = 0.0000 - DV/DL = 0.4640 + DV/DL = 0.4439 ------------------------------------------------------------------------------ - Softcore part of the system: 1 atoms, TEMP(K) = 159.58 - SC_Etot= 0.3123 SC_EKtot= 0.4757 SC_EPtot = 0.7093 - SC_BOND= 0.3122 SC_ANGLE= 0.0629 SC_DIHED = 0.5897 - SC_14NB= 0.0187 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 1 atoms, TEMP(K) = 159.45 + SC_Etot= 0.3188 SC_EKtot= 0.4753 SC_EPtot = 0.7054 + SC_BOND= 0.3124 SC_ANGLE= 0.0680 SC_DIHED = 0.5903 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0853 SC_DERIV = 0.0853 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0868 SC_DERIV = 0.0868 ------------------------------------------------------------------------------ @@ -500,22 +523,22 @@ Total charge of -0.04433900 removed from 3 atoms NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 301.93 PRESS = 0.0 - Etot = -73136.3168 EKtot = 18319.5644 EPtot = -91455.8812 - BOND = 481.6195 ANGLE = 1235.6667 DIHED = 1759.5665 - 1-4 NB = 610.3718 1-4 EEL = 6272.4707 VDWAALS = 11248.2670 - EELEC = -113063.8434 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = -73136.2005 EKtot = 18319.5983 EPtot = -91455.7988 + BOND = 481.6466 ANGLE = 1235.6530 DIHED = 1759.5668 + 1-4 NB = 610.4448 1-4 EEL = 6272.4642 VDWAALS = 11248.2681 + EELEC = -113063.8422 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 299575.9290 Density = 1.0111 - DV/DL = 5.5023 + DV/DL = 5.6191 ------------------------------------------------------------------------------ - Softcore part of the system: 2 atoms, TEMP(K) = 74.20 - SC_Etot= 1.6275 SC_EKtot= 0.3686 SC_EPtot = 1.2589 - SC_BOND= 0.0145 SC_ANGLE= 0.5363 SC_DIHED = 0.5973 - SC_14NB= 0.1108 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 2 atoms, TEMP(K) = 75.51 + SC_Etot= 1.5245 SC_EKtot= 0.3751 SC_EPtot = 1.1494 + SC_BOND= 0.0151 SC_ANGLE= 0.5373 SC_DIHED = 0.5970 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6622 SC_DERIV = 2.6622 + SC_EEL_DER= 0.0000 SC_VDW_DER= 2.6588 SC_DERIV = 2.6588 ------------------------------------------------------------------------------ @@ -523,22 +546,22 @@ Total charge of -0.04433900 removed from 3 atoms NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 3.00 PRESS = 0.0 - Etot = 1.8791 EKtot = 182.1373 EPtot = 183.9548 - BOND = 16.5570 ANGLE = 47.8689 DIHED = 12.3665 - 1-4 NB = 1.5073 1-4 EEL = 7.9590 VDWAALS = 23.9856 - EELEC = 178.5900 EHBOND = 0.0000 RESTRAINT = 0.0000 + Etot = 1.7616 EKtot = 182.1600 EPtot = 183.8524 + BOND = 16.5545 ANGLE = 47.8871 DIHED = 12.3656 + 1-4 NB = 1.4622 1-4 EEL = 7.9564 VDWAALS = 23.9838 + EELEC = 178.5895 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 0.0039 Density = 0.0000 - DV/DL = 0.4640 + DV/DL = 0.4439 ------------------------------------------------------------------------------ - Softcore part of the system: 2 atoms, TEMP(K) = 25.31 - SC_Etot= 0.1455 SC_EKtot= 0.1257 SC_EPtot = 0.1759 - SC_BOND= 0.0183 SC_ANGLE= 0.1455 SC_DIHED = 0.2073 - SC_14NB= 0.1329 SC_14EEL= 0.0000 SC_VDW = 0.0000 + Softcore part of the system: 2 atoms, TEMP(K) = 24.90 + SC_Etot= 0.1480 SC_EKtot= 0.1237 SC_EPtot = 0.1311 + SC_BOND= 0.0183 SC_ANGLE= 0.1477 SC_DIHED = 0.2070 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 SC_EEL = 0.0000 SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 - SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0853 SC_DERIV = 0.0853 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0868 SC_DERIV = 0.0868 ------------------------------------------------------------------------------ @@ -546,13 +569,13 @@ Total charge of -0.04433900 removed from 3 atoms NSTEP = 20 TIME(PS) = 250.020 TEMP(K) = 3.00 PRESS = 0.0 - Etot = 0.0000 EKtot = 0.0000 EPtot = 2.7694 + Etot = 0.0000 EKtot = 0.0000 EPtot = 2.8026 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 - 1-4 NB = 0.0000 1-4 EEL = -8.1252 VDWAALS = -1.5836 - EELEC = 12.5489 EHBOND = 0.0000 RESTRAINT = 0.0000 + 1-4 NB = 0.1246 1-4 EEL = -8.1289 VDWAALS = -1.5853 + EELEC = 12.5499 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 0.0000 Density = 0.0000 - DV/DL = 2.7694 + DV/DL = 2.8026 ------------------------------------------------------------------------------ | MC Barostat: 2 volume changes attempted. @@ -567,15 +590,15 @@ Total charge of -0.04433900 removed from 3 atoms | | Routine Sec % | ------------------------------ -| Nonbond 0.02 13.51 +| Nonbond 0.01 8.02 | Bond 0.00 0.00 | Angle 0.00 0.00 | Dihedral 0.00 0.00 -| Shake 0.00 2.70 -| RunMD 0.12 83.78 -| Other 0.00 0.00 +| Shake 0.00 0.09 +| RunMD 0.11 90.24 +| Other 0.00 1.66 | ------------------------------ -| Total 0.15 +| Total 0.12 | PME Nonbond Pairlist CPU Time: | @@ -592,9 +615,9 @@ Total charge of -0.04433900 removed from 3 atoms | --------------------------------- | NonBonded Calc 0.00 0.00 | Exclude Masked 0.00 0.00 -| Other 0.00 0.00 +| Other 0.00 0.03 | --------------------------------- -| Total 0.00 0.00 +| Total 0.00 0.03 | PME Reciprocal Force CPU Time: | @@ -611,17 +634,17 @@ Total charge of -0.04433900 removed from 3 atoms | Final Performance Info: | ----------------------------------------------------- | Average timings for last 15 steps: -| Elapsed(s) = 0.13 Per Step(ms) = 8.99 -| ns/day = 9.61 seconds/ns = 8990.06 +| Elapsed(s) = 0.11 Per Step(ms) = 7.25 +| ns/day = 11.92 seconds/ns = 7247.27 | | Average timings for all steps: -| Elapsed(s) = 0.15 Per Step(ms) = 7.50 -| ns/day = 11.52 seconds/ns = 7496.90 +| Elapsed(s) = 0.12 Per Step(ms) = 5.83 +| ns/day = 14.83 seconds/ns = 5825.85 | ----------------------------------------------------- -| Setup CPU time: 1.02 seconds -| NonSetup CPU time: 0.15 seconds -| Total CPU time: 1.17 seconds 0.00 hours +| Setup CPU time: 0.52 seconds +| NonSetup CPU time: 0.12 seconds +| Total CPU time: 0.63 seconds 0.00 hours | Setup wall time: 1 seconds | NonSetup wall time: 0 seconds diff --git test/cuda/gti/SC_Correction/complex/Run.SC_NVE test/cuda/gti/SC_Correction/complex/Run.SC_NVE new file mode 100755 index 0000000000..91a3d5f1ab --- /dev/null +++ test/cuda/gti/SC_Correction/complex/Run.SC_NVE @@ -0,0 +1,98 @@ +#!/bin/csh -f +#TEST-PROGRAM pmemd.cuda +#TEST-DESCRIP signle ion non-softcore TI +#TEST-PURPOSE regression, basic +#TEST-STATE undocumented + +#$1 = PREC_MODEL +#$2 = NETCDF +echo `pwd` + + +if ( "$1" == "CPU" ) then + set sander = "mpiexec -np 20 ${AMBERHOME}/bin/pmemd.MPI" +else + set sander = ${AMBERHOME}/bin/pmemd.cuda_$1 +endif + + +cat > mdin < mdin < mdin <