------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 06/28/2006 at 14:36:02 [-O]verwriting output File Assignments: | MDIN: initial-md.in | MDOUT: complex-init-md.out |INPCRD: complex-min2.rst | PARM: complex.top |RESTRT: complex-init-md.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Initial MD equilibration &cntrl imin=0, irest=0, nstlim=2000,dt=0.001, ntc=1, ntpr=100, ntwx=100, cut=16, ntb=0, igb=1, ntt=3, gamma_ln=1.0, tempi=0.0, temp0=300.0, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 06/28/06 Time = 12:01:19 NATOM = 3900 NTYPES = 17 NBONH = 2058 MBONA = 1848 NTHETH = 4120 MTHETA = 2493 NPHIH = 7513 MPHIA = 4818 NHPARM = 0 NPARM = 0 NNB = 20316 NRES = 332 NBONA = 1848 NTHETA = 2493 NPHIA = 4818 NUMBND = 45 NUMANG = 97 NPTRA = 45 NATYP = 31 NPHB = 1 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 97609 | Hollerith 23734 | Integer 208220 | Max Pairs 1 | Max Rstack 1 | Max Istack 1 | Total 1668 kbytes | 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 = 100, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 100, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 1, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 16.00000, 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 = 25.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 2000, 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 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 75 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -13252.9253 EKtot = 0.0000 EPtot = -13252.9253 BOND = 188.3262 ANGLE = 535.3873 DIHED = 1712.3179 1-4 NB = 716.3484 1-4 EEL = 4213.2028 VDWAALS = -2084.4035 EELEC = -15193.0930 EGB = -3341.0112 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 100 TIME(PS) = 0.100 TEMP(K) = 32.26 PRESS = 0.0 Etot = -12585.4934 EKtot = 374.7754 EPtot = -12960.2688 BOND = 304.4434 ANGLE = 645.3347 DIHED = 1739.8367 1-4 NB = 737.9100 1-4 EEL = 4223.5046 VDWAALS = -2067.7215 EELEC = -15406.0090 EGB = -3137.5677 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 200 TIME(PS) = 0.200 TEMP(K) = 59.82 PRESS = 0.0 Etot = -11987.5982 EKtot = 695.0006 EPtot = -12682.5988 BOND = 410.4499 ANGLE = 768.2534 DIHED = 1771.5005 1-4 NB = 735.3440 1-4 EEL = 4194.5956 VDWAALS = -2030.4251 EELEC = -15092.1793 EGB = -3440.1378 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 300 TIME(PS) = 0.300 TEMP(K) = 85.45 PRESS = 0.0 Etot = -11443.8744 EKtot = 992.8973 EPtot = -12436.7717 BOND = 496.5145 ANGLE = 872.5543 DIHED = 1792.3905 1-4 NB = 742.5430 1-4 EEL = 4195.8273 VDWAALS = -2024.5487 EELEC = -14460.3728 EGB = -4051.6799 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 400 TIME(PS) = 0.400 TEMP(K) = 105.30 PRESS = 0.0 Etot = -10991.5273 EKtot = 1223.4533 EPtot = -12214.9806 BOND = 591.1718 ANGLE = 963.8886 DIHED = 1825.9594 1-4 NB = 748.5433 1-4 EEL = 4177.4625 VDWAALS = -2032.5390 EELEC = -14812.4562 EGB = -3677.0110 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 500 TIME(PS) = 0.500 TEMP(K) = 122.40 PRESS = 0.0 Etot = -10573.5150 EKtot = 1422.1913 EPtot = -11995.7063 BOND = 661.3062 ANGLE = 1072.2942 DIHED = 1848.7746 1-4 NB = 752.1491 1-4 EEL = 4200.8145 VDWAALS = -1990.2955 EELEC = -15862.0665 EGB = -2678.6828 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 600 TIME(PS) = 0.600 TEMP(K) = 139.74 PRESS = 0.0 Etot = -10167.7543 EKtot = 1623.6023 EPtot = -11791.3566 BOND = 751.7389 ANGLE = 1132.8205 DIHED = 1861.4436 1-4 NB = 750.7184 1-4 EEL = 4159.6978 VDWAALS = -2003.6986 EELEC = -15154.1779 EGB = -3289.8994 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 700 TIME(PS) = 0.700 TEMP(K) = 155.69 PRESS = 0.0 Etot = -9814.6087 EKtot = 1809.0084 EPtot = -11623.6172 BOND = 799.0375 ANGLE = 1198.4583 DIHED = 1878.7715 1-4 NB = 764.6089 1-4 EEL = 4188.6490 VDWAALS = -1957.8493 EELEC = -15462.7403 EGB = -3032.5527 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 800 TIME(PS) = 0.800 TEMP(K) = 165.74 PRESS = 0.0 Etot = -9520.2570 EKtot = 1925.7088 EPtot = -11445.9658 BOND = 900.0625 ANGLE = 1258.4583 DIHED = 1897.4562 1-4 NB = 760.5820 1-4 EEL = 4131.3471 VDWAALS = -1971.2507 EELEC = -15389.6582 EGB = -3032.9631 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 900 TIME(PS) = 0.900 TEMP(K) = 182.72 PRESS = 0.0 Etot = -9253.0143 EKtot = 2123.0258 EPtot = -11376.0401 BOND = 886.8120 ANGLE = 1331.4720 DIHED = 1900.2755 1-4 NB = 747.6317 1-4 EEL = 4153.6619 VDWAALS = -1923.5104 EELEC = -14555.0810 EGB = -3917.3018 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ KE Trans = 0.5108 KE Rot = 0.5902 C.O.M. Vel = 0.006020 Translational and rotational motion removed KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000 NSTEP = 1000 TIME(PS) = 1.000 TEMP(K) = 192.78 PRESS = 0.0 Etot = -9002.9466 EKtot = 2239.8768 EPtot = -11242.8234 BOND = 941.0721 ANGLE = 1362.3649 DIHED = 1934.9501 1-4 NB = 763.7003 1-4 EEL = 4139.7845 VDWAALS = -1953.2571 EELEC = -14358.6952 EGB = -4072.7431 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 1100 TIME(PS) = 1.100 TEMP(K) = 195.65 PRESS = 0.0 Etot = -8773.1011 EKtot = 2273.2417 EPtot = -11046.3428 BOND = 1010.2272 ANGLE = 1426.2144 DIHED = 1942.2690 1-4 NB = 765.3516 1-4 EEL = 4162.3733 VDWAALS = -1922.4820 EELEC = -13452.3682 EGB = -4977.9282 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 1200 TIME(PS) = 1.200 TEMP(K) = 209.81 PRESS = 0.0 Etot = -8533.2695 EKtot = 2437.8577 EPtot = -10971.1272 BOND = 1007.8179 ANGLE = 1492.3883 DIHED = 1954.0669 1-4 NB = 754.3163 1-4 EEL = 4146.9501 VDWAALS = -1892.2366 EELEC = -13328.1793 EGB = -5106.2508 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 1300 TIME(PS) = 1.300 TEMP(K) = 218.27 PRESS = 0.0 Etot = -8314.9073 EKtot = 2536.1142 EPtot = -10851.0215 BOND = 1100.1125 ANGLE = 1513.2790 DIHED = 1962.8266 1-4 NB = 766.1824 1-4 EEL = 4119.4944 VDWAALS = -1901.9027 EELEC = -13824.3757 EGB = -4586.6380 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 1400 TIME(PS) = 1.400 TEMP(K) = 223.78 PRESS = 0.0 Etot = -8174.3135 EKtot = 2600.0968 EPtot = -10774.4103 BOND = 1168.0877 ANGLE = 1515.9644 DIHED = 1970.7837 1-4 NB = 766.7306 1-4 EEL = 4164.7521 VDWAALS = -1897.6944 EELEC = -13656.1394 EGB = -4806.8949 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 1500 TIME(PS) = 1.500 TEMP(K) = 232.21 PRESS = 0.0 Etot = -8009.3700 EKtot = 2698.0322 EPtot = -10707.4022 BOND = 1135.8052 ANGLE = 1579.1925 DIHED = 1990.1019 1-4 NB = 790.7430 1-4 EEL = 4151.8233 VDWAALS = -1915.8464 EELEC = -12994.2221 EGB = -5444.9996 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 1600 TIME(PS) = 1.600 TEMP(K) = 237.22 PRESS = 0.0 Etot = -7859.9445 EKtot = 2756.2653 EPtot = -10616.2098 BOND = 1164.6475 ANGLE = 1598.6125 DIHED = 1987.7676 1-4 NB = 788.9516 1-4 EEL = 4147.1364 VDWAALS = -1904.8818 EELEC = -12957.7467 EGB = -5440.6969 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 1700 TIME(PS) = 1.700 TEMP(K) = 245.46 PRESS = 0.0 Etot = -7704.1777 EKtot = 2852.0678 EPtot = -10556.2455 BOND = 1197.7125 ANGLE = 1675.3866 DIHED = 1983.1228 1-4 NB = 777.9760 1-4 EEL = 4079.5774 VDWAALS = -1877.7288 EELEC = -13175.0159 EGB = -5217.2762 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 1800 TIME(PS) = 1.800 TEMP(K) = 254.00 PRESS = 0.0 Etot = -7578.7545 EKtot = 2951.2346 EPtot = -10529.9891 BOND = 1194.3569 ANGLE = 1686.0504 DIHED = 1991.8219 1-4 NB = 787.2405 1-4 EEL = 4146.1281 VDWAALS = -1891.4478 EELEC = -12778.7132 EGB = -5665.4261 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 1900 TIME(PS) = 1.900 TEMP(K) = 256.05 PRESS = 0.0 Etot = -7490.2445 EKtot = 2975.1256 EPtot = -10465.3701 BOND = 1226.8124 ANGLE = 1684.6169 DIHED = 2005.6613 1-4 NB = 795.2641 1-4 EEL = 4144.5768 VDWAALS = -1885.0547 EELEC = -13535.7323 EGB = -4901.5147 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ KE Trans = 0.6800 KE Rot = 0.2072 C.O.M. Vel = 0.006946 Translational and rotational motion removed KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000 NSTEP = 2000 TIME(PS) = 2.000 TEMP(K) = 259.73 PRESS = 0.0 Etot = -7397.7415 EKtot = 3017.8080 EPtot = -10415.5495 BOND = 1247.2719 ANGLE = 1697.5582 DIHED = 2003.4568 1-4 NB = 777.4050 1-4 EEL = 4162.7282 VDWAALS = -1886.9507 EELEC = -13279.0090 EGB = -5138.0099 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ A V E R A G E S O V E R 2000 S T E P S NSTEP = 2000 TIME(PS) = 2.000 TEMP(K) = 172.44 PRESS = 0.0 Etot = -9401.4567 EKtot = 2003.5569 EPtot = -11405.0136 BOND = 888.7912 ANGLE = 1291.7441 DIHED = 1904.8140 1-4 NB = 760.2383 1-4 EEL = 4153.3906 VDWAALS = -1948.3765 EELEC = -14243.6866 EGB = -4211.9287 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 2000 TIME(PS) = 2.000 TEMP(K) = 70.85 PRESS = 0.0 Etot = 1623.0103 EKtot = 823.2339 EPtot = 800.4021 BOND = 298.3686 ANGLE = 325.9954 DIHED = 85.2637 1-4 NB = 18.1045 1-4 EEL = 34.6986 VDWAALS = 62.1725 EELEC = 928.9203 EGB = 891.9056 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 1558.21 (27.92% of Gen B) | Calc gb diag 2985.64 (53.50% of Gen B) | Calc gb off-diag 1036.56 (18.57% of Gen B) | Gen Born time 5580.46 (100.0% of Nonbo) | Nonbond force 5580.46 (99.64% of Force) | Bond/Angle/Dihedral 20.31 ( 0.36% of Force) | Force time 5600.83 (99.80% of Runmd) | Verlet update time 11.21 ( 0.20% of Runmd) | Runmd Time 5612.06 (100.0% of Total) | Total time 5612.35 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 14:36:02.037 on 06/28/2006 | Setup done at 14:36:02.334 on 06/28/2006 | Run done at 16:09:34.396 on 06/28/2006 | wallclock() was called 36024 times