------------------------------------------------------- Amber 14 SANDER 2014 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 11 | Run on 06/21/2011 at 14:31:57 | WARNING: Stack usage limited by a hard resource limit of 536870912 bytes! | If segment violations occur, get your sysadmin to increase the limit. [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: mdout.ips | INPCRD: inpcrd | PARM: prmtop | RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo Here is the input file: check of isotropic periodic sum simulation, ntb=2 &cntrl imin=0, ntx=5, ntpr=1, nscm=5000,iwrap=1, ntf=2, ntc=2, ntb=2, ntp=1, tautp=5.0, taup=5.0, nstlim=20, t=0.0, dt=0.002, cut=10.0, ntt=1, irest=1 ips=1, / | Conditional Compilation Defines Used: | DIRFRC_COMTRANS | DIRFRC_EFS | DIRFRC_NOVEC | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | MKL | Largest sphere to fit in unit cell has radius = 27.755 | INFO: Old style PARM file read | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting new box info from bottom of inpcrd NATOM = 24030 NTYPES = 18 NBONH = 23393 MBONA = 682 NTHETH = 805 MTHETA = 1049 NPHIH = 1416 MPHIA = 1695 NHPARM = 0 NPARM = 0 NNB = 36045 NRES = 7742 NBONA = 682 NTHETA = 1049 NPHIA = 1695 NUMBND = 39 NUMANG = 76 NPTRA = 34 NATYP = 28 NPHB = 1 IFBOX = 2 NMXRS = 34 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 10 10 10 | Direct force subcell size = 6.7985 6.7985 6.7985 BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 5, irest = 1, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 500 iwrap = 1, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, 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 = 10.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 20, nscm = 5000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Berendsen (weak-coupling) temperature regulation: temp0 = 300.00000, tempi = 0.00000, tautp = 5.00000 Pressure regulation: ntp = 1 pres0 = 1.00000, comp = 44.60000, taup = 5.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 | 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 = 0 vdwmeth = 2, eedmeth = 6, netfrc = 1 Box X = 67.985 Box Y = 67.985 Box Z = 67.985 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 72 NFFT2 = 72 NFFT3 = 72 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 7684 Sum of charges from parm topology file = 0.00000017 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 848299 | Integers 631705 | Nonbonded Pairs Initial Allocation: 7268474 ---------------------------------- Using 3D-IPS algorithm IPS Radius: 10.00 A Using IPS for electrostatic energy Using IPS for L-J energy ---------------------------------- -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- eedmeth=6: Using IPS method for electrostatic energy | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960 --------------------------------------------------- |--------------------------------------------------- | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.33 | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.80 |--------------------------------------------------- NSTEP = 1 TIME(PS) = 0.002 TEMP(K) = 301.40 PRESS = -140.8 Etot = -67902.7529 EKtot = 14582.3834 EPtot = -82485.1363 BOND = 236.3050 ANGLE = 523.8042 DIHED = 542.6053 1-4 NB = 264.7708 1-4 EEL = -3290.5712 VDWAALS = 10292.3333 EELEC = -91054.3837 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6966.9758 VIRIAL = 7702.1396 VOLUME = 241885.2000 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 2 TIME(PS) = 0.004 TEMP(K) = 300.81 PRESS = -124.2 Etot = -67902.7658 EKtot = 14553.7414 EPtot = -82456.5072 BOND = 232.1604 ANGLE = 524.0316 DIHED = 538.1730 1-4 NB = 266.0853 1-4 EEL = -3296.5777 VDWAALS = 10299.2087 EELEC = -91019.5885 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6960.2461 VIRIAL = 7609.1107 VOLUME = 241884.5882 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 3 TIME(PS) = 0.006 TEMP(K) = 300.08 PRESS = -111.0 Etot = -67902.6112 EKtot = 14518.6553 EPtot = -82421.2666 BOND = 237.3457 ANGLE = 516.2701 DIHED = 533.5307 1-4 NB = 265.9600 1-4 EEL = -3299.7721 VDWAALS = 10306.6530 EELEC = -90981.2539 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6953.2012 VIRIAL = 7532.8668 VOLUME = 241884.0478 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 4 TIME(PS) = 0.008 TEMP(K) = 299.29 PRESS = -102.8 Etot = -67901.9683 EKtot = 14480.3524 EPtot = -82382.3207 BOND = 247.2836 ANGLE = 505.8108 DIHED = 530.1103 1-4 NB = 264.1048 1-4 EEL = -3298.9273 VDWAALS = 10314.5205 EELEC = -90945.2232 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6946.1819 VIRIAL = 7483.1881 VOLUME = 241883.5645 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 298.60 PRESS = -100.3 Etot = -67901.6274 EKtot = 14446.6742 EPtot = -82348.3017 BOND = 250.1433 ANGLE = 500.0221 DIHED = 528.7477 1-4 NB = 260.9690 1-4 EEL = -3294.1971 VDWAALS = 10322.5368 EELEC = -90916.5235 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6939.6288 VIRIAL = 7463.4898 VOLUME = 241883.1165 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 6 TIME(PS) = 0.012 TEMP(K) = 298.07 PRESS = -102.2 Etot = -67901.9626 EKtot = 14421.1291 EPtot = -82323.0917 BOND = 242.7300 ANGLE = 501.5699 DIHED = 529.3179 1-4 NB = 257.6646 1-4 EEL = -3286.6466 VDWAALS = 10331.3189 EELEC = -90899.0464 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6933.9726 VIRIAL = 7467.8655 VOLUME = 241882.6793 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 7 TIME(PS) = 0.014 TEMP(K) = 297.62 PRESS = -106.0 Etot = -67902.1429 EKtot = 14399.2599 EPtot = -82301.4028 BOND = 234.4620 ANGLE = 507.6976 DIHED = 531.1891 1-4 NB = 255.2598 1-4 EEL = -3277.5750 VDWAALS = 10342.0648 EELEC = -90894.5012 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6929.4515 VIRIAL = 7482.8348 VOLUME = 241882.2339 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 8 TIME(PS) = 0.016 TEMP(K) = 297.19 PRESS = -107.8 Etot = -67901.6723 EKtot = 14378.7439 EPtot = -82280.4163 BOND = 233.1870 ANGLE = 512.7300 DIHED = 533.7199 1-4 NB = 254.1079 1-4 EEL = -3268.3302 VDWAALS = 10355.4815 EELEC = -90901.3125 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6925.9410 VIRIAL = 7489.0889 VOLUME = 241881.7723 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 9 TIME(PS) = 0.018 TEMP(K) = 296.91 PRESS = -103.1 Etot = -67901.3143 EKtot = 14365.3753 EPtot = -82266.6896 BOND = 234.8545 ANGLE = 512.2852 DIHED = 536.3308 1-4 NB = 253.6972 1-4 EEL = -3260.4143 VDWAALS = 10371.2863 EELEC = -90914.7293 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6922.8979 VIRIAL = 7461.4320 VOLUME = 241881.3027 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 296.87 PRESS = -87.0 Etot = -67901.7989 EKtot = 14363.3931 EPtot = -82265.1920 BOND = 231.4288 ANGLE = 507.2313 DIHED = 538.4495 1-4 NB = 253.3909 1-4 EEL = -3255.2752 VDWAALS = 10388.2627 EELEC = -90928.6800 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6919.4834 VIRIAL = 7373.7741 VOLUME = 241880.8534 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 11 TIME(PS) = 0.022 TEMP(K) = 296.93 PRESS = -57.0 Etot = -67902.5151 EKtot = 14366.1098 EPtot = -82268.6248 BOND = 223.8338 ANGLE = 502.6563 DIHED = 539.4478 1-4 NB = 253.2131 1-4 EEL = -3253.7160 VDWAALS = 10405.0657 EELEC = -90939.1255 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6914.8640 VIRIAL = 7212.7074 VOLUME = 241880.4737 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 12 TIME(PS) = 0.024 TEMP(K) = 296.88 PRESS = -15.6 Etot = -67902.3754 EKtot = 14363.4902 EPtot = -82265.8656 BOND = 220.8287 ANGLE = 502.4079 DIHED = 538.6928 1-4 NB = 253.5666 1-4 EEL = -3255.4808 VDWAALS = 10421.0580 EELEC = -90946.9389 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6908.5781 VIRIAL = 6989.9589 VOLUME = 241880.2233 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 13 TIME(PS) = 0.026 TEMP(K) = 296.73 PRESS = 29.6 Etot = -67901.3103 EKtot = 14356.5173 EPtot = -82257.8275 BOND = 226.6672 ANGLE = 505.8397 DIHED = 536.1515 1-4 NB = 254.2620 1-4 EEL = -3259.4453 VDWAALS = 10436.2523 EELEC = -90957.5548 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6900.7849 VIRIAL = 6746.2902 VOLUME = 241880.1518 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 14 TIME(PS) = 0.028 TEMP(K) = 296.77 PRESS = 67.0 Etot = -67900.4466 EKtot = 14358.1755 EPtot = -82258.6221 BOND = 236.7079 ANGLE = 508.5235 DIHED = 532.8748 1-4 NB = 254.3127 1-4 EEL = -3264.2704 VDWAALS = 10450.3392 EELEC = -90977.1097 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6892.2520 VIRIAL = 6542.2263 VOLUME = 241880.2751 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 297.19 PRESS = 87.1 Etot = -67900.7834 EKtot = 14378.7836 EPtot = -82279.5670 BOND = 245.6676 ANGLE = 505.8958 DIHED = 530.4345 1-4 NB = 253.1196 1-4 EEL = -3269.0246 VDWAALS = 10461.8496 EELEC = -91007.5095 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6884.0859 VIRIAL = 6429.0967 VOLUME = 241880.5600 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 16 TIME(PS) = 0.032 TEMP(K) = 297.90 PRESS = 87.8 Etot = -67901.9807 EKtot = 14413.1847 EPtot = -82315.1654 BOND = 253.2764 ANGLE = 498.5772 DIHED = 530.0650 1-4 NB = 251.1226 1-4 EEL = -3273.3811 VDWAALS = 10468.9485 EELEC = -91043.7740 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6877.3302 VIRIAL = 6418.8739 VOLUME = 241880.9316 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 17 TIME(PS) = 0.034 TEMP(K) = 298.56 PRESS = 74.8 Etot = -67902.9558 EKtot = 14444.7975 EPtot = -82347.7533 BOND = 259.8587 ANGLE = 492.9342 DIHED = 532.2029 1-4 NB = 249.1124 1-4 EEL = -3277.4566 VDWAALS = 10470.9899 EELEC = -91075.3948 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6872.6179 VIRIAL = 6481.7326 VOLUME = 241881.3061 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 18 TIME(PS) = 0.036 TEMP(K) = 298.87 PRESS = 57.1 Etot = -67903.1337 EKtot = 14459.8319 EPtot = -82362.9656 BOND = 262.4629 ANGLE = 494.2028 DIHED = 536.2011 1-4 NB = 247.8157 1-4 EEL = -3281.5652 VDWAALS = 10468.8533 EELEC = -91090.9362 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6870.0414 VIRIAL = 6572.0168 VOLUME = 241881.6248 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 19 TIME(PS) = 0.038 TEMP(K) = 298.77 PRESS = 40.8 Etot = -67902.8164 EKtot = 14455.0160 EPtot = -82357.8324 BOND = 259.1706 ANGLE = 500.4428 DIHED = 540.6405 1-4 NB = 247.3772 1-4 EEL = -3285.8668 VDWAALS = 10464.1590 EELEC = -91083.7557 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6869.2885 VIRIAL = 6656.2033 VOLUME = 241881.8667 Density = 1.0205 ------------------------------------------------------------------------------ wrapping first mol.: -45.32286 32.04811 55.50894 NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 298.34 PRESS = 28.6 Etot = -67902.3530 EKtot = 14434.2497 EPtot = -82336.6026 BOND = 253.7744 ANGLE = 505.7182 DIHED = 544.3803 1-4 NB = 247.1628 1-4 EEL = -3289.9871 VDWAALS = 10458.2107 EELEC = -91055.8620 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6869.9391 VIRIAL = 6720.7860 VOLUME = 241882.0384 Density = 1.0205 ------------------------------------------------------------------------------ A V E R A G E S O V E R 20 S T E P S NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 298.19 PRESS = -34.3 Etot = -67902.0643 EKtot = 14426.9932 EPtot = -82329.0576 BOND = 241.1074 ANGLE = 506.4326 DIHED = 535.1633 1-4 NB = 255.3538 1-4 EEL = -3276.9240 VDWAALS = 10391.4696 EELEC = -90981.6602 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6912.8881 VIRIAL = 7091.7841 VOLUME = 241881.9405 Density = 1.0205 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 1.35 PRESS = 81.2 Etot = 0.7067 EKtot = 65.1964 EPtot = 65.6336 BOND = 12.0002 ANGLE = 8.1083 DIHED = 4.5177 1-4 NB = 5.9050 1-4 EEL = 15.1633 VDWAALS = 64.6205 EELEC = 65.2923 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 31.2584 VIRIAL = 452.9055 VOLUME = 1.4639 Density = 0.0000 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 5.28 97.78 | Bond 0.00 0.00 | Angle 0.00 0.09 | Dihedral 0.01 0.15 | Shake 0.03 0.52 | RunMD 0.08 1.46 | Other 0.00 0.00 | ------------------------------ | Total 5.40 | PME Nonbond Pairlist CPU Time: | | Routine Sec % | --------------------------------- | Set Up Cit 0.00 0.07 | Build List 0.82 15.29 | --------------------------------- | Total 0.83 15.36 | PME Direct Force CPU Time: | | Routine Sec % | --------------------------------- | NonBonded Calc 4.40 81.63 | Exclude Masked 0.00 0.00 | Other 0.04 0.78 | --------------------------------- | Total 4.45 82.41 | PME Reciprocal Force CPU Time: | | Routine Sec % | --------------------------------- | 1D bspline 0.00 0.00 | Grid Charges 0.00 0.00 | Scalar Sum 0.00 0.00 | Gradient Sum 0.00 0.00 | FFT 0.00 0.00 | --------------------------------- | Total 0.00 0.00 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 19 steps: | Elapsed(s) = 5.05 Per Step(ms) = 265.76 | ns/day = 0.65 seconds/ns = 132878.39 | | Average timings for all steps: | Elapsed(s) = 5.46 Per Step(ms) = 273.03 | ns/day = 0.63 seconds/ns = 136516.08 | ----------------------------------------------------- | Setup CPU time: 0.10 seconds | NonSetup CPU time: 5.40 seconds | Total CPU time: 5.49 seconds 0.00 hours | Setup wall time: 0 seconds | NonSetup wall time: 6 seconds | Total wall time: 6 seconds 0.00 hours