------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 11 | Run on 04/14/2010 at 00:34:21 | 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: myoglobin_md.out.CPU | INPCRD: inpcrd | PARM: prmtop | RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo Here is the input file: &cntrl imin=0,irest=1,ntx=5, nstlim=20,dt=0.002,ntb=0, ntf=2,ntc=2,tol=0.000001, ntpr=1, ntwx=0, ntwr=25, cut=9999.0, rgbmax=15.0, igb=1,ntt=0,nscm=0, / | Conditional Compilation Defines Used: | DIRFRC_COMTRANS | DIRFRC_EFS | DIRFRC_NOVEC | PUBFFT | FFTLOADBAL_2PROC | MKL | New format PARM file being parsed. | Version = 1.000 Date = 09/17/01 Time = 12:09:08 | 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: -------------------------------------------------------------------------------- NATOM = 2492 NTYPES = 14 NBONH = 1275 MBONA = 1245 NTHETH = 2900 MTHETA = 1673 NPHIH = 5168 MPHIA = 2923 NHPARM = 0 NPARM = 0 NNB = 13801 NRES = 153 NBONA = 1245 NTHETA = 1673 NPHIA = 2923 NUMBND = 38 NUMANG = 88 NPTRA = 31 NATYP = 25 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 -------------------------------------------------------------------------------- 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 = 25 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 0, igb = 1, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut =9999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500 rdt = 0.00000, rgbmax = 15.00000 extdiel = 78.50000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 20, nscm = 0, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00000 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 1 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 1.500 ps Number of triangulated 3-point waters found: 0 | Dynamic Memory, Types Used: | Reals 69269 | Integers 224834 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP = 1 TIME(PS) = 1.502 TEMP(K) = 305.20 PRESS = 0.0 Etot = -1294.9940 EKtot = 1880.4186 EPtot = -3175.4126 BOND = 446.2716 ANGLE = 1444.5851 DIHED = 800.1506 1-4 NB = 526.9513 1-4 EEL = 7881.6446 VDWAALS = -1151.3755 EELEC = -382.5872 EGB = -12741.0531 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 2 TIME(PS) = 1.504 TEMP(K) = 323.85 PRESS = 0.0 Etot = -1303.3803 EKtot = 1995.3422 EPtot = -3298.7224 BOND = 421.8234 ANGLE = 1362.9993 DIHED = 795.9318 1-4 NB = 522.7646 1-4 EEL = 7886.8376 VDWAALS = -1158.5895 EELEC = -391.3211 EGB = -12739.1686 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 3 TIME(PS) = 1.506 TEMP(K) = 319.59 PRESS = 0.0 Etot = -1300.2887 EKtot = 1969.0872 EPtot = -3269.3759 BOND = 437.0008 ANGLE = 1388.0980 DIHED = 794.2315 1-4 NB = 521.0911 1-4 EEL = 7888.8486 VDWAALS = -1163.3516 EELEC = -395.6029 EGB = -12739.6915 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 4 TIME(PS) = 1.508 TEMP(K) = 298.87 PRESS = 0.0 Etot = -1289.8977 EKtot = 1841.4074 EPtot = -3131.3051 BOND = 472.7925 ANGLE = 1491.7619 DIHED = 795.8971 1-4 NB = 522.2883 1-4 EEL = 7887.4243 VDWAALS = -1164.2728 EELEC = -395.1476 EGB = -12742.0489 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 5 TIME(PS) = 1.510 TEMP(K) = 284.35 PRESS = 0.0 Etot = -1284.1832 EKtot = 1751.9319 EPtot = -3036.1151 BOND = 488.3079 ANGLE = 1568.3661 DIHED = 799.7907 1-4 NB = 523.4628 1-4 EEL = 7883.0272 VDWAALS = -1163.1563 EELEC = -391.1204 EGB = -12744.7930 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 6 TIME(PS) = 1.512 TEMP(K) = 288.88 PRESS = 0.0 Etot = -1288.7260 EKtot = 1779.8514 EPtot = -3068.5774 BOND = 471.2261 ANGLE = 1551.4551 DIHED = 804.1887 1-4 NB = 522.0114 1-4 EEL = 7876.7654 VDWAALS = -1162.3581 EELEC = -385.0860 EGB = -12746.7801 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 7 TIME(PS) = 1.514 TEMP(K) = 302.89 PRESS = 0.0 Etot = -1297.1575 EKtot = 1866.2172 EPtot = -3163.3746 BOND = 447.6017 ANGLE = 1479.3755 DIHED = 808.2920 1-4 NB = 519.0791 1-4 EEL = 7870.3054 VDWAALS = -1161.8886 EELEC = -378.3336 EGB = -12747.8061 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 8 TIME(PS) = 1.516 TEMP(K) = 308.26 PRESS = 0.0 Etot = -1299.2281 EKtot = 1899.2544 EPtot = -3198.4825 BOND = 441.6097 ANGLE = 1444.0356 DIHED = 812.0633 1-4 NB = 517.6910 1-4 EEL = 7865.5808 VDWAALS = -1159.1406 EELEC = -372.0364 EGB = -12748.2858 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 9 TIME(PS) = 1.518 TEMP(K) = 300.22 PRESS = 0.0 Etot = -1293.5881 EKtot = 1849.7412 EPtot = -3143.3294 BOND = 444.7508 ANGLE = 1484.2867 DIHED = 815.2369 1-4 NB = 518.6797 1-4 EEL = 7864.1563 VDWAALS = -1154.5886 EELEC = -367.4303 EGB = -12748.4208 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 10 TIME(PS) = 1.520 TEMP(K) = 290.58 PRESS = 0.0 Etot = -1288.3395 EKtot = 1790.3252 EPtot = -3078.6647 BOND = 436.4759 ANGLE = 1545.5658 DIHED = 817.1030 1-4 NB = 520.5824 1-4 EEL = 7866.5403 VDWAALS = -1151.4077 EELEC = -365.5093 EGB = -12748.0150 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 11 TIME(PS) = 1.522 TEMP(K) = 290.79 PRESS = 0.0 Etot = -1289.4382 EKtot = 1791.6685 EPtot = -3081.1067 BOND = 420.7545 ANGLE = 1550.6804 DIHED = 817.3213 1-4 NB = 522.4396 1-4 EEL = 7871.8399 VDWAALS = -1150.6555 EELEC = -366.4691 EGB = -12747.0178 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 12 TIME(PS) = 1.524 TEMP(K) = 298.90 PRESS = 0.0 Etot = -1294.1953 EKtot = 1841.5945 EPtot = -3135.7898 BOND = 421.1059 ANGLE = 1491.1173 DIHED = 816.4945 1-4 NB = 524.4973 1-4 EEL = 7878.0859 VDWAALS = -1151.7444 EELEC = -369.4661 EGB = -12745.8802 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 13 TIME(PS) = 1.526 TEMP(K) = 304.60 PRESS = 0.0 Etot = -1296.6919 EKtot = 1876.7198 EPtot = -3173.4118 BOND = 442.6971 ANGLE = 1430.8025 DIHED = 815.9238 1-4 NB = 526.7655 1-4 EEL = 7883.0735 VDWAALS = -1154.5420 EELEC = -373.1290 EGB = -12745.0032 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 14 TIME(PS) = 1.528 TEMP(K) = 301.98 PRESS = 0.0 Etot = -1295.2667 EKtot = 1860.5808 EPtot = -3155.8474 BOND = 461.3697 ANGLE = 1430.8056 DIHED = 816.9117 1-4 NB = 528.8884 1-4 EEL = 7885.2472 VDWAALS = -1158.5498 EELEC = -376.4556 EGB = -12744.0647 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 15 TIME(PS) = 1.530 TEMP(K) = 293.88 PRESS = 0.0 Etot = -1292.2519 EKtot = 1810.6582 EPtot = -3102.9101 BOND = 456.8857 ANGLE = 1488.9994 DIHED = 819.7230 1-4 NB = 530.7768 1-4 EEL = 7884.1241 VDWAALS = -1162.0381 EELEC = -379.0989 EGB = -12742.2821 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 16 TIME(PS) = 1.532 TEMP(K) = 287.22 PRESS = 0.0 Etot = -1290.1329 EKtot = 1769.6270 EPtot = -3059.7599 BOND = 440.0987 ANGLE = 1549.0614 DIHED = 823.0906 1-4 NB = 531.8480 1-4 EEL = 7880.2968 VDWAALS = -1163.9783 EELEC = -381.1539 EGB = -12739.0232 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 17 TIME(PS) = 1.534 TEMP(K) = 286.95 PRESS = 0.0 Etot = -1290.2829 EKtot = 1767.9888 EPtot = -3058.2717 BOND = 435.5645 ANGLE = 1557.3394 DIHED = 825.2277 1-4 NB = 530.9485 1-4 EEL = 7875.1852 VDWAALS = -1165.3212 EELEC = -382.8793 EGB = -12734.3366 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 18 TIME(PS) = 1.536 TEMP(K) = 292.56 PRESS = 0.0 Etot = -1292.8075 EKtot = 1802.5522 EPtot = -3095.3598 BOND = 447.7693 ANGLE = 1513.3277 DIHED = 825.7645 1-4 NB = 527.8754 1-4 EEL = 7870.5611 VDWAALS = -1167.0189 EELEC = -384.5056 EGB = -12729.1333 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 19 TIME(PS) = 1.538 TEMP(K) = 298.38 PRESS = 0.0 Etot = -1295.5199 EKtot = 1838.3927 EPtot = -3133.9126 BOND = 458.6438 ANGLE = 1467.3103 DIHED = 826.3377 1-4 NB = 524.6772 1-4 EEL = 7867.8775 VDWAALS = -1168.2356 EELEC = -386.0827 EGB = -12724.4406 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 20 TIME(PS) = 1.540 TEMP(K) = 298.46 PRESS = 0.0 Etot = -1295.7731 EKtot = 1838.8797 EPtot = -3134.6529 BOND = 455.9620 ANGLE = 1465.7063 DIHED = 828.6543 1-4 NB = 523.8816 1-4 EEL = 7867.6477 VDWAALS = -1168.1115 EELEC = -387.2517 EGB = -12721.1416 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ A V E R A G E S O V E R 20 S T E P S NSTEP = 20 TIME(PS) = 1.540 TEMP(K) = 298.82 PRESS = 0.0 Etot = -1293.6072 EKtot = 1841.1120 EPtot = -3134.7191 BOND = 447.4356 ANGLE = 1485.2840 DIHED = 812.9167 1-4 NB = 524.3600 1-4 EEL = 7876.7535 VDWAALS = -1160.0162 EELEC = -380.5333 EGB = -12740.9193 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 20 TIME(PS) = 1.540 TEMP(K) = 10.07 PRESS = 0.0 Etot = 4.4965 EKtot = 62.0709 EPtot = 66.2350 BOND = 17.1920 ANGLE = 56.4635 DIHED = 10.8056 1-4 NB = 4.0792 1-4 EEL = 7.9433 VDWAALS = 5.6892 EELEC = 9.1102 EGB = 7.7534 RESTRAINT = 0.0000 |E(PBS) = 0.2598 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 8.47 98.76 | Bond 0.00 0.00 | Angle 0.01 0.15 | Dihedral 0.06 0.76 | Shake 0.00 0.01 | RunMD 0.03 0.31 | Other 0.00 0.00 | ------------------------------ | Total 8.58 | Generalized Born CPU Time: | | Routine Sec % | ------------------------------------ | Radii Calc 1.75 20.42 | Diagonal Calc 2.60 30.27 | Off Diagonal Calc 4.12 48.00 | --------------------------------- | Total 8.46 98.68 | Setup CPU time: 0.06 seconds | NonSetup CPU time: 8.58 seconds | Total CPU time: 8.64 seconds 0.00 hours | Setup wall time: 0 seconds | NonSetup wall time: 9 seconds | Total wall time: 9 seconds 0.00 hours