------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 12 | Run on 10/01/2012 at 17:13:53 [-O]verwriting output File Assignments: | MDIN: mdin_min.120 | MDOUT: ala_tri_min_120.out | INPCRD: 03_equil.rst | PARM: ala_tri.prmtop | RESTRT: ala_tri_min_120.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo |LOGFILE: logfile Here is the input file: 2000 step minimization for 120 deg &cntrl imin = 1, maxcyc=2000, ncyc = 500, ntpr = 100, ntwr = 1000, ntf = 1, ntc = 1, cut = 8.0, ntb = 1, ntp = 0, nmropt = 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 = 1, nmropt = 1 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 100, ntrx = 1, ntwr = 1000 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 1, 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 Energy minimization: maxcyc = 2000, ncyc = 500, ntmin = 1 dx0 = 0.01000, drms = 0.00010 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 = 1 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 0 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 = 120.000 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 222836 | Integers 176381 | 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 ENERGY RMS GMAX NAME NUMBER 1 -8.2649E+03 1.5463E+01 2.8723E+02 N 17 BOND = 10.4264 ANGLE = 13.8736 DIHED = 20.9150 VDWAALS = 1319.2179 EEL = -9902.4511 HBOND = 0.0000 1-4 VDW = 3.7074 1-4 EEL = 115.3924 RESTRAINT = 153.9907 EAMBER = -8418.9184 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 153.991 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.0336E+04 1.9490E+00 7.5790E+01 C 15 BOND = 672.4226 ANGLE = 8.5975 DIHED = 26.3940 VDWAALS = 1164.1268 EEL = -12334.5210 HBOND = 0.0000 1-4 VDW = 3.5989 1-4 EEL = 115.5529 RESTRAINT = 7.6061 EAMBER = -10343.8284 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 7.606 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 200 -1.0608E+04 1.8287E+00 8.0904E+01 C 5 BOND = 727.8253 ANGLE = 9.3577 DIHED = 27.8543 VDWAALS = 1282.9800 EEL = -12777.4175 HBOND = 0.0000 1-4 VDW = 3.6465 1-4 EEL = 115.6896 RESTRAINT = 2.0834 EAMBER = -10610.0642 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 2.083 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 300 -1.0748E+04 1.4012E+00 5.5987E+01 C 5 BOND = 734.2039 ANGLE = 7.7244 DIHED = 27.9174 VDWAALS = 1383.7126 EEL = -13023.1750 HBOND = 0.0000 1-4 VDW = 3.5307 1-4 EEL = 115.9520 RESTRAINT = 1.8952 EAMBER = -10750.1339 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 1.895 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 400 -1.0843E+04 1.1307E+00 4.9980E+01 C 15 BOND = 756.6189 ANGLE = 6.4320 DIHED = 27.7686 VDWAALS = 1465.1385 EEL = -13221.1753 HBOND = 0.0000 1-4 VDW = 3.5904 1-4 EEL = 115.9792 RESTRAINT = 2.2328 EAMBER = -10845.6477 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 2.233 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 500 -1.0912E+04 9.4733E-01 3.5212E+01 C 15 BOND = 769.7698 ANGLE = 6.7537 DIHED = 28.3275 VDWAALS = 1528.7061 EEL = -13366.6691 HBOND = 0.0000 1-4 VDW = 3.5822 1-4 EEL = 116.0435 RESTRAINT = 1.0478 EAMBER = -10913.4863 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 1.048 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 600 -1.1138E+04 6.3665E-01 1.2533E+01 N 17 BOND = 829.0314 ANGLE = 5.1753 DIHED = 28.5049 VDWAALS = 1795.7083 EEL = -13917.3453 HBOND = 0.0000 1-4 VDW = 3.6588 1-4 EEL = 116.0548 RESTRAINT = 1.0545 EAMBER = -11139.2117 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 1.054 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 700 -1.1188E+04 7.6022E-01 1.2539E+01 CB 11 BOND = 839.4778 ANGLE = 4.8032 DIHED = 28.4711 VDWAALS = 1847.6993 EEL = -14030.0553 HBOND = 0.0000 1-4 VDW = 3.6515 1-4 EEL = 116.2866 RESTRAINT = 1.1705 EAMBER = -11189.6659 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 1.170 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 800 -1.1234E+04 2.4956E-01 3.8241E+00 C 25 BOND = 848.4276 ANGLE = 4.5172 DIHED = 28.5214 VDWAALS = 1895.6739 EEL = -14132.0489 HBOND = 0.0000 1-4 VDW = 3.6363 1-4 EEL = 116.4018 RESTRAINT = 1.1099 EAMBER = -11234.8707 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 1.110 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 900 -1.1266E+04 2.9967E-01 6.7489E+00 C 25 BOND = 856.2346 ANGLE = 4.5196 DIHED = 28.5367 VDWAALS = 1936.1829 EEL = -14212.5969 HBOND = 0.0000 1-4 VDW = 3.6366 1-4 EEL = 116.3716 RESTRAINT = 1.0200 EAMBER = -11267.1150 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 1.020 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1000 -1.1291E+04 3.0886E-01 8.6027E+00 C 25 BOND = 862.0410 ANGLE = 4.4614 DIHED = 28.5019 VDWAALS = 1967.5572 EEL = -14274.6175 HBOND = 0.0000 1-4 VDW = 3.6375 1-4 EEL = 116.4316 RESTRAINT = 0.9843 EAMBER = -11291.9870 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.984 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1100 -1.1312E+04 1.8821E-01 3.7622E+00 N 17 BOND = 867.6320 ANGLE = 4.3611 DIHED = 28.4132 VDWAALS = 1999.7380 EEL = -14333.3535 HBOND = 0.0000 1-4 VDW = 3.6527 1-4 EEL = 116.4878 RESTRAINT = 0.9992 EAMBER = -11313.0688 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.999 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1200 -1.1331E+04 2.6645E-01 7.1712E+00 C 25 BOND = 872.6190 ANGLE = 4.2218 DIHED = 28.2523 VDWAALS = 2028.1697 EEL = -14385.7383 HBOND = 0.0000 1-4 VDW = 3.6840 1-4 EEL = 116.4558 RESTRAINT = 1.1091 EAMBER = -11332.3358 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 1.109 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1300 -1.1345E+04 3.2120E-01 8.2751E+00 C 25 BOND = 876.2206 ANGLE = 4.5430 DIHED = 28.3009 VDWAALS = 2050.0158 EEL = -14425.4694 HBOND = 0.0000 1-4 VDW = 3.6889 1-4 EEL = 116.5990 RESTRAINT = 0.9312 EAMBER = -11346.1011 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.931 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1400 -1.1355E+04 1.9497E-01 3.6730E+00 H 28 BOND = 878.5088 ANGLE = 4.2733 DIHED = 28.2705 VDWAALS = 2062.5016 EEL = -14449.8689 HBOND = 0.0000 1-4 VDW = 3.7452 1-4 EEL = 116.7822 RESTRAINT = 0.9675 EAMBER = -11355.7874 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.967 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1500 -1.1365E+04 2.7439E-01 5.7842E+00 N 17 BOND = 881.3200 ANGLE = 4.1077 DIHED = 28.3567 VDWAALS = 2073.1595 EEL = -14473.4668 HBOND = 0.0000 1-4 VDW = 3.8022 1-4 EEL = 117.0892 RESTRAINT = 0.8895 EAMBER = -11365.6315 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.889 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1600 -1.1375E+04 3.1567E-01 7.3996E+00 C 15 BOND = 883.8542 ANGLE = 3.7779 DIHED = 28.1901 VDWAALS = 2084.3054 EEL = -14497.6252 HBOND = 0.0000 1-4 VDW = 3.8688 1-4 EEL = 117.2662 RESTRAINT = 1.1324 EAMBER = -11376.3627 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 1.132 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1700 -1.1385E+04 3.8036E-01 8.6988E+00 N 17 BOND = 885.2479 ANGLE = 4.0725 DIHED = 28.1711 VDWAALS = 2091.7164 EEL = -14515.9774 HBOND = 0.0000 1-4 VDW = 3.9518 1-4 EEL = 117.3206 RESTRAINT = 0.9092 EAMBER = -11385.4973 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.909 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1800 -1.1395E+04 7.4476E-01 1.8877E+01 C 15 BOND = 890.8245 ANGLE = 3.5192 DIHED = 28.5491 VDWAALS = 2109.1056 EEL = -14549.3747 HBOND = 0.0000 1-4 VDW = 3.7848 1-4 EEL = 117.3214 RESTRAINT = 1.1462 EAMBER = -11396.2701 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 1.146 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1900 -1.1408E+04 3.2355E-01 7.6508E+00 CH3 29 BOND = 891.1974 ANGLE = 3.6972 DIHED = 28.2125 VDWAALS = 2122.6051 EEL = -14576.1392 HBOND = 0.0000 1-4 VDW = 3.9566 1-4 EEL = 117.2951 RESTRAINT = 0.9722 EAMBER = -11409.1753 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.972 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 2000 -1.1417E+04 3.4874E-01 1.0045E+01 H1 1747 BOND = 893.7049 ANGLE = 3.9655 DIHED = 28.1562 VDWAALS = 2132.2354 EEL = -14597.5095 HBOND = 0.0000 1-4 VDW = 3.9857 1-4 EEL = 117.4102 RESTRAINT = 1.1698 EAMBER = -11418.0516 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 1.170 =============================================================================== Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 2000 -1.1417E+04 3.4874E-01 1.0045E+01 H1 1747 BOND = 893.7049 ANGLE = 3.9655 DIHED = 28.1562 VDWAALS = 2132.2354 EEL = -14597.5095 HBOND = 0.0000 1-4 VDW = 3.9857 1-4 EEL = 117.4102 RESTRAINT = 1.1698 EAMBER = -11418.0516 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 1.170 =============================================================================== -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines, Average for All Tasks: | | Routine Sec % | ------------------------------ | DataDistrib 0.67 2.79 | Nonbond 23.35 96.65 | Bond 0.04 0.19 | Angle 0.01 0.02 | Dihedral 0.03 0.10 | Shake 0.00 0.00 | Other 0.06 0.25 | ------------------------------ | Total 24.16 | PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | Set Up Cit 0.00 0.00 | Build List 0.85 3.50 | --------------------------------- | Total 0.85 3.50 | PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | NonBonded Calc 15.71 65.00 | Exclude Masked 0.15 0.62 | Other 0.13 0.54 | --------------------------------- | Total 15.99 66.16 | PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | 1D bspline 0.34 1.43 | Grid Charges 0.27 1.14 | Scalar Sum 2.10 8.69 | Gradient Sum 0.45 1.84 | FFT 3.34 13.82 | --------------------------------- | Total 6.50 26.92 | 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 1 steps: | Elapsed(s) = 24.23 Per Step(ms) = 24233.35 | ns/day = 0.00 seconds/ns = ********** | | Average timings for all steps: | Elapsed(s) = 24.23 Per Step(ms) = 24233.35 | ns/day = 0.00 seconds/ns = ********** | ----------------------------------------------------- | Master Setup CPU time: 0.04 seconds | Master NonSetup CPU time: 24.11 seconds | Master Total CPU time: 24.15 seconds 0.01 hours | Master Setup wall time: 0 seconds | Master NonSetup wall time: 25 seconds | Master Total wall time: 25 seconds 0.01 hours