------------------------------------------------------- Amber 7 SANDER Scripps/UCSF 2002 ------------------------------------------------------- | Mon Feb 25 00:11:36 2002 [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: trx.md.out |INPCRD: trx.equil.rst | PARM: trx.top |RESTRT: trx.md.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: trx.md.x |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: run MD at 300K &cntrl ntc=2, ntf=2, cut=12.0, igb=2, saltcon=0.2, gbsa=1, ntpr=50, ntwx=50, nstlim = 500, dt=0.002, ntt=1, tempi=300.0, temp0=300.0, tautp=2.0, ntx=1, irest=0, ntb=0, nscm = 1000, &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 02/21/02 Time = 19:40:40 NATOM = 1654 NTYPES = 14 NBONH = 832 MBONA = 838 NTHETH = 1911 MTHETA = 1138 NPHIH = 3535 MPHIA = 2155 NHPARM = 0 NPARM = 0 NNB = 9195 NRES = 108 NBONA = 838 NTHETA = 1138 NPHIA = 2155 NUMBND = 42 NUMANG = 91 NPTRA = 42 NATYP = 27 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 | Memory Use Allocated Used | Real 2000000 49759 | Hollerith 400000 10034 | Integer 2000000 157178 | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 50, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 0, igb = 2, nsnb = 25 ipol = 0, gbsa = 1 dielc = 1.00000, cut = 12.00000, intdiel = 1.00000 saltcon = 0.20000, offset = 0.09000, gbalpha= 0.80000 gbbeta = 0.00000, gbgamma = 2.90912, surften = 0.00500 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 500, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Temperature regulation: ig = 71277, ntt = 1, vrand = 0 temp0 = 300.00000, tempi = 300.00000, heat = 0.00000 dtemp = 5.00000, tautp = 2.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 10.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP = 0 TIME(PS) = 10.000 TEMP(K) = 357.80 PRESS = 0.0 Etot = -850.0885 EKtot = 1466.1089 EPtot = -2316.1973 BOND = 277.9680 ANGLE = 730.5613 DIHED = 1038.0380 1-4 NB = 376.7587 1-4 EEL = 5889.7917 VDWAALS = -802.0918 EELEC = -8122.3703 EGB = -1732.8817 RESTRAINT = 0.0000 ESURF = 28.0286 ------------------------------------------------------------------------------ NSTEP = 50 TIME(PS) = 10.100 TEMP(K) = 276.51 PRESS = 0.0 Etot = -1090.0435 EKtot = 1133.0415 EPtot = -2223.0850 BOND = 295.0318 ANGLE = 813.9603 DIHED = 1060.8734 1-4 NB = 370.9811 1-4 EEL = 5896.2997 VDWAALS = -791.3810 EELEC = -8113.6718 EGB = -1784.1431 RESTRAINT = 0.0000 ESURF = 28.9646 ------------------------------------------------------------------------------ NSTEP = 100 TIME(PS) = 10.200 TEMP(K) = 279.71 PRESS = 0.0 Etot = -1088.1285 EKtot = 1146.1414 EPtot = -2234.2698 BOND = 314.7333 ANGLE = 841.1668 DIHED = 992.2429 1-4 NB = 369.9782 1-4 EEL = 5859.9376 VDWAALS = -789.9021 EELEC = -7985.7293 EGB = -1865.9436 RESTRAINT = 0.0000 ESURF = 29.2463 ------------------------------------------------------------------------------ NSTEP = 150 TIME(PS) = 10.300 TEMP(K) = 286.46 PRESS = 0.0 Etot = -1087.4270 EKtot = 1173.7921 EPtot = -2261.2191 BOND = 295.3673 ANGLE = 815.3719 DIHED = 1004.7713 1-4 NB = 379.7957 1-4 EEL = 5831.2907 VDWAALS = -785.8942 EELEC = -8165.1137 EGB = -1666.3557 RESTRAINT = 0.0000 ESURF = 29.5477 ------------------------------------------------------------------------------ NSTEP = 200 TIME(PS) = 10.400 TEMP(K) = 287.06 PRESS = 0.0 Etot = -1084.1773 EKtot = 1176.2642 EPtot = -2260.4415 BOND = 307.9275 ANGLE = 796.0185 DIHED = 1009.5828 1-4 NB = 364.8985 1-4 EEL = 5857.3134 VDWAALS = -775.5520 EELEC = -8033.8530 EGB = -1817.4708 RESTRAINT = 0.0000 ESURF = 30.6937 ------------------------------------------------------------------------------ NSTEP = 250 TIME(PS) = 10.500 TEMP(K) = 284.12 PRESS = 0.0 Etot = -1081.6764 EKtot = 1164.1910 EPtot = -2245.8674 BOND = 324.7257 ANGLE = 800.6275 DIHED = 994.6250 1-4 NB = 364.2583 1-4 EEL = 5903.4485 VDWAALS = -779.9984 EELEC = -8096.8208 EGB = -1787.7427 RESTRAINT = 0.0000 ESURF = 31.0096 ------------------------------------------------------------------------------ NSTEP = 300 TIME(PS) = 10.600 TEMP(K) = 283.20 PRESS = 0.0 Etot = -1077.9117 EKtot = 1160.4543 EPtot = -2238.3660 BOND = 325.1413 ANGLE = 804.4260 DIHED = 994.8233 1-4 NB = 342.1454 1-4 EEL = 5880.0590 VDWAALS = -758.4046 EELEC = -7786.2754 EGB = -2072.1250 RESTRAINT = 0.0000 ESURF = 31.8441 ------------------------------------------------------------------------------ NSTEP = 350 TIME(PS) = 10.700 TEMP(K) = 280.54 PRESS = 0.0 Etot = -1074.0747 EKtot = 1149.5175 EPtot = -2223.5922 BOND = 274.7721 ANGLE = 834.2781 DIHED = 1019.7577 1-4 NB = 360.1178 1-4 EEL = 5852.1351 VDWAALS = -750.5147 EELEC = -7567.0030 EGB = -2279.3599 RESTRAINT = 0.0000 ESURF = 32.2247 ------------------------------------------------------------------------------ NSTEP = 400 TIME(PS) = 10.800 TEMP(K) = 289.84 PRESS = 0.0 Etot = -1072.9465 EKtot = 1187.6583 EPtot = -2260.6048 BOND = 292.3704 ANGLE = 780.7673 DIHED = 980.9034 1-4 NB = 374.9288 1-4 EEL = 5841.6801 VDWAALS = -744.3629 EELEC = -7763.2175 EGB = -2056.2782 RESTRAINT = 0.0000 ESURF = 32.6038 ------------------------------------------------------------------------------ NSTEP = 450 TIME(PS) = 10.900 TEMP(K) = 291.22 PRESS = 0.0 Etot = -1068.4891 EKtot = 1193.2806 EPtot = -2261.7697 BOND = 324.4074 ANGLE = 762.1379 DIHED = 1001.9675 1-4 NB = 353.4192 1-4 EEL = 5868.6733 VDWAALS = -740.1224 EELEC = -7575.4554 EGB = -2289.5160 RESTRAINT = 0.0000 ESURF = 32.7188 ------------------------------------------------------------------------------ NSTEP = 500 TIME(PS) = 11.000 TEMP(K) = 277.30 PRESS = 0.0 Etot = -1064.7948 EKtot = 1136.2583 EPtot = -2201.0532 BOND = 328.6610 ANGLE = 830.5852 DIHED = 1003.0739 1-4 NB = 366.0819 1-4 EEL = 5848.0776 VDWAALS = -760.0772 EELEC = -7666.0293 EGB = -2184.7253 RESTRAINT = 0.0000 ESURF = 33.2991 ------------------------------------------------------------------------------ A V E R A G E S O V E R 500 S T E P S NSTEP = 500 TIME(PS) = 11.000 TEMP(K) = 285.57 PRESS = 0.0 Etot = -1080.2663 EKtot = 1170.1455 EPtot = -2250.4119 BOND = 310.1242 ANGLE = 795.0717 DIHED = 1008.0418 1-4 NB = 366.3237 1-4 EEL = 5870.7958 VDWAALS = -773.0006 EELEC = -7834.1371 EGB = -2024.6004 RESTRAINT = 0.0000 ESURF = 30.9690 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 500 TIME(PS) = 11.000 TEMP(K) = 4.89 PRESS = 0.0 Etot = 8.5249 EKtot = 20.0266 EPtot = 21.3773 BOND = 15.2001 ANGLE = 19.5540 DIHED = 20.2587 1-4 NB = 7.1295 1-4 EEL = 22.3600 VDWAALS = 20.5977 EELEC = 237.3006 EGB = 231.0619 RESTRAINT = 0.0000 ESURF = 1.5623 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 357.31 (14.22% of Gen B) | Calc gb diag 1306.79 (51.99% of Gen B) | Calc gb off-diag 536.65 (21.35% of Gen B) | Surface area energy 312.70 (12.44% of Gen B) | Gen Born time 2513.45 (100.0% of Nonbo) | Nonbond force 2513.45 (99.11% of Force) | Bond energy 0.34 ( 0.01% of Force) | Angle energy 5.01 ( 0.20% of Force) | Dihedral energy 17.22 ( 0.68% of Force) | Force time 2536.03 (100.0% of Runmd) | Shake time 0.90 ( 0.04% of Runmd) | Verlet update time 0.89 ( 0.04% of Runmd) | Runmd Time 2537.82 (100.0% of Total) | Total time 2226.75 (100.0% of ALL ) | Highest rstack allocated: 18194 | Highest istack allocated: 6616 | Setup wallclock 1 seconds | Nonsetup wallclock 2295 seconds