------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | Run on 12/13/2008 at 14:32:15 [-O]verwriting output File Assignments: | MDIN: md1.in | MDOUT: md1.out |INPCRD: pep.crd | PARM: pep.top |RESTRT: md1.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: md1.crd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | Here is the input file: comp: 20ns MD &cntrl imin = 0, irest=0, ntx=1, nstlim = 500, dt = 0.002, ntt = 3, gamma_ln = 1.0, ig = -1, tempi = 300.0, temp0 = 300.00 ntc = 2, ntf = 2, tol = 0.00001, ntb = 0, ntr = 0, ntwx = 500, ntwe = 0, ntwr =500, ntpr = 500, igb=5, gbsa=1, cut = 999., rgbmax = 999., nscm = 1000, extdiel=4, &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 12/01/08 Time = 15:18:42 NATOM = 3655 NTYPES = 13 NBONH = 1858 MBONA = 1845 NTHETH = 4196 MTHETA = 2520 NPHIH = 7914 MPHIA = 5797 NHPARM = 0 NPARM = 0 NNB = 20228 NRES = 232 NBONA = 1845 NTHETA = 2520 NPHIA = 5797 NUMBND = 34 NUMANG = 78 NPTRA = 45 NATYP = 23 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are H(N)-modified Bondi radii (mbondi2) | Memory Use Allocated | Real 208752 | Hollerith 22164 | Integer 357777 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 3115 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 = 500, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 500, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 0, igb = 5, nsnb = 25 ipol = 0, gbsa = 1, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00500 rdt = 0.00000, rgbmax = 999.00000 extdiel = 4.00000 alpb = 0 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 Langevin dynamics temperature regulation: ig = 921074 temp0 = 300.00000, tempi = 300.00000, gamma_ln= 1.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- | # of SOLUTE degrees of freedom (RNDFP): 9107. | # of SOLVENT degrees of freedom (RNDFS): 0. | NDFMIN = 9107. NUM_NOSHAKE = 0 CORRECTED RNDFP = 9107. | TOTAL # of degrees of freedom (RNDF) = 9107. NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 371.16 PRESS = 0.0 Etot = -7116.5804 EKtot = 3358.4705 EPtot = -10475.0509 BOND = 104.3950 ANGLE = 340.6627 DIHED = 2193.0413 1-4 NB = 782.7417 1-4 EEL = 9135.8815 VDWAALS = -2026.1780 EELEC = -20147.3069 EGB = -913.4167 RESTRAINT = 0.0000 ESURF= 55.1285 ------------------------------------------------------------------------------ NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 253.23 PRESS = 0.0 Etot = -6092.6433 EKtot = 2291.4110 EPtot = -8384.0542 BOND = 649.6881 ANGLE = 1590.5530 DIHED = 2515.9502 1-4 NB = 879.3790 1-4 EEL = 8691.4021 VDWAALS = -1710.9759 EELEC = -20210.5437 EGB = -848.6231 RESTRAINT = 0.0000 ESURF= 59.1161 ------------------------------------------------------------------------------ A V E R A G E S O V E R 500 S T E P S NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 218.84 PRESS = 0.0 Etot = -6731.5512 EKtot = 1980.2028 EPtot = -8711.7540 BOND = 552.1168 ANGLE = 1405.9631 DIHED = 2483.4170 1-4 NB = 860.1537 1-4 EEL = 8734.2334 VDWAALS = -1762.0401 EELEC = -20162.9927 EGB = -880.4928 RESTRAINT = 0.0000 ESURF= 57.8876 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 25.91 PRESS = 0.0 Etot = 436.0912 EKtot = 234.4185 EPtot = 232.4609 BOND = 58.6311 ANGLE = 141.5403 DIHED = 36.5353 1-4 NB = 14.6362 1-4 EEL = 55.5384 VDWAALS = 48.7708 EELEC = 78.0612 EGB = 25.8004 RESTRAINT = 0.0000 ESURF= 1.2085 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 262.17 (16.34% of Gen B) | Calc gb diag 580.70 (36.20% of Gen B) | Calc gb off-diag 643.43 (40.11% of Gen B) | Surface area energy 117.91 ( 7.35% of Gen B) | Gen Born time 1604.22 (100.0% of Nonbo) | Nonbond force 1604.22 (99.80% of Force) | Bond/Angle/Dihedral 3.26 ( 0.20% of Force) | Force time 1607.48 (100.0% of Runmd) | Shake time 0.25 ( 0.02% of Runmd) | Verlet update time 1.07 ( 0.07% of Runmd) | Runmd Time 1608.87 (100.0% of Total) | Other 0.18 ( 0.01% of Total) | Total time 1609.08 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 14:32:15.740 on 12/13/2008 | Setup done at 14:32:15.957 on 12/13/2008 | Run done at 14:59:04.827 on 12/13/2008 | wallclock() was called 13030 times