------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 12 | Run on 10/01/2012 at 17:36:14 [-O]verwriting output File Assignments: | MDIN: mdin_equi.120 | MDOUT: ala_tri_equil_120.out | INPCRD: ala_tri_min_120.rst | PARM: ala_tri.prmtop | RESTRT: ala_tri_equil_120.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo |LOGFILE: logfile Here is the input file: 50 ps NPT equilibration for 120 deg &cntrl imin = 0, ntx = 1, irest = 0, ntpr = 5000, ntwr = 50000, ntwx = 0, ntf = 2, ntc = 2, cut = 8.0, ntb = 2, nstlim = 50000, dt = 0.001, tempi=0.0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0, ntp = 1, pres0 = 1.0, taup = 5.0, nmropt = 1, ioutfm=1, &end &wt type='END', &end DISANG=disang.120 | Conditional Compilation Defines Used: | DIRFRC_COMTRANS | DIRFRC_EFS | DIRFRC_NOVEC | MPI | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | Largest sphere to fit in unit cell has radius = 13.401 | New format PARM file being parsed. | Version = 1.000 Date = 10/01/12 Time = 16:17:26 | Note: 1-4 EEL scale factors are being read from the topology file. | Note: 1-4 VDW scale factors are being read from the topology file. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting new box info from bottom of inpcrd NATOM = 2681 NTYPES = 9 NBONH = 2666 MBONA = 14 NTHETH = 36 MTHETA = 18 NPHIH = 64 MPHIA = 45 NHPARM = 0 NPARM = 0 NNB = 3684 NRES = 887 NBONA = 14 NTHETA = 18 NPHIA = 45 NUMBND = 10 NUMANG = 16 NPTRA = 19 NATYP = 9 NPHB = 1 IFBOX = 2 NMXRS = 10 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 5 5 5 | Direct force subcell size = 6.5650 6.5650 6.5650 BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- ACE General flags: imin = 0, nmropt = 1 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 5000, ntrx = 1, ntwr = 50000 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 2, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 50000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 71277 temp0 = 300.00000, tempi = 0.00000, gamma_ln= 1.00000 Pressure regulation: ntp = 1 pres0 = 1.00000, comp = 44.60000, taup = 5.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 NMR refinement options: iscale = 0, noeskp = 1, ipnlty = 1, mxsub = 1 scalm = 100.00000, pencut = 0.10000, tausw = 0.10000 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 5000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 32.825 Box Y = 32.825 Box Z = 32.825 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 | PMEMD ewald parallel performance parameters: | block_fft = 0 | fft_blk_y_divisor = 2 | excl_recip = 0 | excl_master = 0 | atm_redist_freq = 320 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- ACE begin time read from input coords = 0.000 ps Begin reading energy term weight changes/NMR restraints WEIGHT CHANGES: ** No weight changes given ** RESTRAINTS: Requested file redirections: DISANG = disang.120 Restraints will be read from file: disang.120 Here are comments from the DISANG input file: Number of restraints read = 1 Done reading weight changes/NMR restraints Number of triangulated 3-point waters found: 883 Sum of charges from parm topology file = 0.00000000 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 316330 | Integers 185327 | Nonbonded Pairs Initial Allocation: 305634 | Running AMBER/MPI version on 2 nodes -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION using 5000.0 points per unit in tabled values TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- |--------------------------------------------------- | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.47 | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.89 |--------------------------------------------------- NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = -6160.5 Etot = -12309.8293 EKtot = 0.0000 EPtot = -12309.8293 BOND = 0.7574 ANGLE = 3.9655 DIHED = 28.1562 1-4 NB = 3.9857 1-4 EEL = 117.4102 VDWAALS = 2132.2354 EELEC = -14597.5095 EHBOND = 0.0000 RESTRAINT = 1.1698 EAMBER (non-restraint) = -12310.9991 EKCMT = 0.0000 VIRIAL = 3621.5203 VOLUME = 27226.8598 Density = 0.9834 Ewald error estimate: 0.1455E-04 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 1.170 =============================================================================== NSTEP = 5000 TIME(PS) = 5.000 TEMP(K) = 291.99 PRESS = -617.2 Etot = -7122.0000 EKtot = 1559.9666 EPtot = -8681.9666 BOND = 3.4170 ANGLE = 12.0698 DIHED = 25.9458 1-4 NB = 6.9302 1-4 EEL = 122.1027 VDWAALS = 1249.6622 EELEC = -10103.5976 EHBOND = 0.0000 RESTRAINT = 1.5032 EAMBER (non-restraint) = -8683.4699 EKCMT = 766.7548 VIRIAL = 1124.4181 VOLUME = 26839.4168 Density = 0.9976 Ewald error estimate: 0.3672E-03 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 1.503 =============================================================================== NSTEP = 10000 TIME(PS) = 10.000 TEMP(K) = 303.40 PRESS = 729.3 Etot = -6850.6057 EKtot = 1620.9316 EPtot = -8471.5373 BOND = 7.6552 ANGLE = 11.4292 DIHED = 31.6221 1-4 NB = 4.9804 1-4 EEL = 122.0799 VDWAALS = 1323.5657 EELEC = -9972.9124 EHBOND = 0.0000 RESTRAINT = 0.0425 EAMBER (non-restraint) = -8471.5798 EKCMT = 809.4694 VIRIAL = 384.4632 VOLUME = 26989.0095 Density = 0.9920 Ewald error estimate: 0.2192E-03 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.043 =============================================================================== NSTEP = 15000 TIME(PS) = 15.000 TEMP(K) = 293.93 PRESS = 315.1 Etot = -6841.5487 EKtot = 1570.3191 EPtot = -8411.8678 BOND = 3.5951 ANGLE = 11.9296 DIHED = 26.4940 1-4 NB = 6.5015 1-4 EEL = 120.3692 VDWAALS = 1259.7517 EELEC = -9840.9960 EHBOND = 0.0000 RESTRAINT = 0.4871 EAMBER (non-restraint) = -8412.3549 EKCMT = 760.6811 VIRIAL = 576.8710 VOLUME = 27019.5447 Density = 0.9909 Ewald error estimate: 0.1112E-03 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.487 =============================================================================== NSTEP = 20000 TIME(PS) = 20.000 TEMP(K) = 305.56 PRESS = 293.4 Etot = -6907.4027 EKtot = 1632.4518 EPtot = -8539.8546 BOND = 2.0819 ANGLE = 19.1877 DIHED = 28.2764 1-4 NB = 3.3984 1-4 EEL = 116.1218 VDWAALS = 1296.9845 EELEC = -10005.9110 EHBOND = 0.0000 RESTRAINT = 0.0058 EAMBER (non-restraint) = -8539.8604 EKCMT = 793.2851 VIRIAL = 621.9665 VOLUME = 27043.3326 Density = 0.9900 Ewald error estimate: 0.6775E-04 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.006 =============================================================================== NSTEP = 25000 TIME(PS) = 25.000 TEMP(K) = 305.66 PRESS = 309.5 Etot = -6815.0034 EKtot = 1633.0206 EPtot = -8448.0240 BOND = 7.6864 ANGLE = 12.3965 DIHED = 32.6533 1-4 NB = 5.2985 1-4 EEL = 119.4484 VDWAALS = 1266.5546 EELEC = -9892.1343 EHBOND = 0.0000 RESTRAINT = 0.0727 EAMBER (non-restraint) = -8448.0967 EKCMT = 802.7007 VIRIAL = 622.2816 VOLUME = 26999.8201 Density = 0.9916 Ewald error estimate: 0.9782E-04 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.073 =============================================================================== NSTEP = 30000 TIME(PS) = 30.000 TEMP(K) = 301.93 PRESS = -443.3 Etot = -6868.9817 EKtot = 1613.0673 EPtot = -8482.0490 BOND = 4.7179 ANGLE = 16.6630 DIHED = 29.5398 1-4 NB = 6.8680 1-4 EEL = 115.9571 VDWAALS = 1208.0902 EELEC = -9864.2126 EHBOND = 0.0000 RESTRAINT = 0.3276 EAMBER (non-restraint) = -8482.3766 EKCMT = 798.5581 VIRIAL = 1057.6566 VOLUME = 27072.5164 Density = 0.9890 Ewald error estimate: 0.3947E-03 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.328 =============================================================================== NSTEP = 35000 TIME(PS) = 35.000 TEMP(K) = 301.62 PRESS = 116.9 Etot = -6878.9385 EKtot = 1611.4296 EPtot = -8490.3681 BOND = 6.4781 ANGLE = 13.4818 DIHED = 28.0644 1-4 NB = 4.4163 1-4 EEL = 118.4414 VDWAALS = 1268.7557 EELEC = -9930.4376 EHBOND = 0.0000 RESTRAINT = 0.4318 EAMBER (non-restraint) = -8490.8000 EKCMT = 768.5790 VIRIAL = 700.1324 VOLUME = 27125.0882 Density = 0.9871 Ewald error estimate: 0.1691E-03 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.432 =============================================================================== NSTEP = 40000 TIME(PS) = 40.000 TEMP(K) = 299.80 PRESS = -155.4 Etot = -6818.6127 EKtot = 1601.7148 EPtot = -8420.3275 BOND = 7.2230 ANGLE = 14.3239 DIHED = 28.0479 1-4 NB = 5.8602 1-4 EEL = 116.0806 VDWAALS = 1218.9243 EELEC = -9811.0334 EHBOND = 0.0000 RESTRAINT = 0.2460 EAMBER (non-restraint) = -8420.5735 EKCMT = 801.1955 VIRIAL = 892.3634 VOLUME = 27179.1024 Density = 0.9851 Ewald error estimate: 0.8547E-04 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.246 =============================================================================== NSTEP = 45000 TIME(PS) = 45.000 TEMP(K) = 303.74 PRESS = -99.5 Etot = -6831.7749 EKtot = 1622.7465 EPtot = -8454.5214 BOND = 5.7246 ANGLE = 15.0487 DIHED = 30.1876 1-4 NB = 7.3144 1-4 EEL = 117.1602 VDWAALS = 1251.6950 EELEC = -9881.7870 EHBOND = 0.0000 RESTRAINT = 0.1351 EAMBER (non-restraint) = -8454.6565 EKCMT = 778.6110 VIRIAL = 836.9540 VOLUME = 27162.8552 Density = 0.9857 Ewald error estimate: 0.1824E-03 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.135 =============================================================================== NSTEP = 50000 TIME(PS) = 50.000 TEMP(K) = 298.27 PRESS = 261.0 Etot = -6896.2010 EKtot = 1593.5386 EPtot = -8489.7397 BOND = 5.4154 ANGLE = 16.7892 DIHED = 26.5768 1-4 NB = 4.1796 1-4 EEL = 111.2146 VDWAALS = 1293.6662 EELEC = -9948.2635 EHBOND = 0.0000 RESTRAINT = 0.6821 EAMBER (non-restraint) = -8490.4217 EKCMT = 785.7949 VIRIAL = 633.5122 VOLUME = 27026.9833 Density = 0.9906 Ewald error estimate: 0.1088E-03 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.682 =============================================================================== A V E R A G E S O V E R 10 S T E P S NSTEP = 50000 TIME(PS) = 50.000 TEMP(K) = 300.59 PRESS = 71.0 Etot = -6883.1069 EKtot = 1605.9187 EPtot = -8489.0256 BOND = 5.3995 ANGLE = 14.3320 DIHED = 28.7408 1-4 NB = 5.5747 1-4 EEL = 117.8976 VDWAALS = 1263.7650 EELEC = -9925.1285 EHBOND = 0.0000 RESTRAINT = 0.3934 EAMBER (non-restraint) = -8489.4190 EKCMT = 786.5630 VIRIAL = 745.0619 VOLUME = 27045.7669 Density = 0.9900 Ewald error estimate: 0.1804E-03 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.682 =============================================================================== R M S F L U C T U A T I O N S NSTEP = 50000 TIME(PS) = 50.000 TEMP(K) = 4.42 PRESS = 381.6 Etot = 85.0085 EKtot = 23.6187 EPtot = 73.2878 BOND = 1.8322 ANGLE = 2.4361 DIHED = 2.1222 1-4 NB = 1.2622 1-4 EEL = 3.1530 VDWAALS = 33.2828 EELEC = 82.4606 EHBOND = 0.0000 RESTRAINT = 0.4236 EAMBER (non-restraint) = 72.8642 EKCMT = 16.2413 VIRIAL = 217.8939 VOLUME = 93.5172 Density = 0.0034 Ewald error estimate: 0.1100E-03 ------------------------------------------------------------------------------ NMR restraints on final step: -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines, Average for All Tasks: | | Routine Sec % | ------------------------------ | DataDistrib 37.66 6.26 | Nonbond 523.50 87.06 | Bond 0.03 0.01 | Angle 0.29 0.05 | Dihedral 0.73 0.12 | Shake 3.90 0.65 | RunMD 35.21 5.86 | Other 0.02 0.00 | ------------------------------ | Total 601.34 | PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | Set Up Cit 0.30 0.05 | Build List 29.56 4.91 | --------------------------------- | Total 29.86 4.96 | PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | NonBonded Calc 354.59 58.97 | Exclude Masked 3.67 0.61 | Other 6.91 1.15 | --------------------------------- | Total 365.16 60.72 | PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | 1D bspline 5.49 0.91 | Grid Charges 7.20 1.20 | Scalar Sum 47.51 7.90 | Gradient Sum 10.32 1.72 | FFT 57.90 9.63 | --------------------------------- | Total 128.43 21.36 | PME Load Balancing CPU Time, Average for All Tasks: | | Routine Sec % | ------------------------------------ | Atom Reassign 0.00 0.00 | Image Reassign 0.00 0.00 | FFT Reassign 0.00 0.00 | ------------------------------------ | Total 0.00 0.00 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 0 steps: | Elapsed(s) = 0.00 Per Step(ms) = Infinity | ns/day = 0.00 seconds/ns = Infinity | | Average timings for all steps: | Elapsed(s) = 602.28 Per Step(ms) = 12.05 | ns/day = 7.17 seconds/ns = 12045.70 | ----------------------------------------------------- | Master Setup CPU time: 0.04 seconds | Master NonSetup CPU time: 600.82 seconds | Master Total CPU time: 600.86 seconds 0.17 hours | Master Setup wall time: 0 seconds | Master NonSetup wall time: 602 seconds | Master Total wall time: 602 seconds 0.17 hours