------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 03/18/2010 at 10:37:39 [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: mdout |INPCRD: min.x | PARM: prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | Here is the input file: Test of constant pH in GB on HEWL &cntrl ig=49, nstlim = 50 cut=30.0, igb=2, saltcon=0.1, ntx=1, irest=0, ntb=0, ntpr=10, dt=0.002, nrespa=1, ntt=1, tempi=300.0, temp0 = 300., tautp=2.0, ntc=2, ntf=2, tol=0.000001, ntwr = 20, icnstph=1, ntcnstph=2, solvph=2.0 / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 04/22/03 Time = 10:56:22 NATOM = 1996 NTYPES = 14 NBONH = 995 MBONA = 1025 NTHETH = 2212 MTHETA = 1389 NPHIH = 4239 MPHIA = 2427 NHPARM = 0 NPARM = 0 NNB = 10904 NRES = 129 NBONA = 1025 NTHETA = 1389 NPHIA = 2427 NUMBND = 40 NUMANG = 90 NPTRA = 40 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 107361 | Hollerith 6119 | Integer 119015 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 1327 kbytes | 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 -------------------------------------------------------------------------------- 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 = 10, ntrx = 1, ntwr = 20 iwrap = 0, ntwx = 0, 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 = 0, iesp = 0 dielc = 1.00000, cut = 30.00000, intdiel = 1.00000 saltcon = 0.10000, offset = 0.09000, gbalpha= 0.80000 gbbeta = 0.00000, gbgamma = 2.90912, surften = 0.00500 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 50, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Berendsen (weak-coupling) temperature regulation: temp0 = 300.00000, tempi = 300.00000, tautp = 2.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00000 Constant pH options: ntcnstph = 2 solvph = 2.00000 reading charge increments from file: cpin | 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): 4993. | # of SOLVENT degrees of freedom (RNDFS): 0. | NDFMIN = 4987. NUM_NOSHAKE = 0 CORRECTED RNDFP = 4987. | TOTAL # of degrees of freedom (RNDF) = 4987. NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 355.72 PRESS = 0.0 Etot = -4105.8987 EKtot = 1762.6242 EPtot = -5868.5229 BOND = 64.4710 ANGLE = 230.5518 DIHED = 830.6145 1-4 NB = 415.5580 1-4 EEL = 3765.5754 VDWAALS = -1096.5582 EELEC = -8750.9534 EGB = -1327.7821 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 151.38 PRESS = 0.0 Etot = -4409.5041 EKtot = 750.0758 EPtot = -5159.5799 BOND = 198.3337 ANGLE = 688.7830 DIHED = 924.9432 1-4 NB = 451.5455 1-4 EEL = 3774.6634 VDWAALS = -1067.8172 EELEC = -8649.0618 EGB = -1480.9696 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 165.49 PRESS = 0.0 Etot = -4391.4686 EKtot = 819.9905 EPtot = -5211.4590 BOND = 207.2323 ANGLE = 613.9408 DIHED = 939.6942 1-4 NB = 436.0210 1-4 EEL = 3762.8577 VDWAALS = -1083.2242 EELEC = -8472.8031 EGB = -1615.1777 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 169.87 PRESS = 0.0 Etot = -4399.5055 EKtot = 841.7323 EPtot = -5241.2378 BOND = 223.0034 ANGLE = 619.7415 DIHED = 930.9337 1-4 NB = 420.4064 1-4 EEL = 3770.2412 VDWAALS = -1077.0992 EELEC = -8498.2638 EGB = -1630.2011 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 173.95 PRESS = 0.0 Etot = -4323.4543 EKtot = 861.9210 EPtot = -5185.3753 BOND = 220.1849 ANGLE = 646.4395 DIHED = 913.5668 1-4 NB = 405.6484 1-4 EEL = 3699.0421 VDWAALS = -1073.4560 EELEC = -8152.2785 EGB = -1844.5226 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 172.05 PRESS = 0.0 Etot = -4327.0520 EKtot = 852.4951 EPtot = -5179.5470 BOND = 234.3066 ANGLE = 667.4015 DIHED = 909.0594 1-4 NB = 400.4914 1-4 EEL = 3721.9845 VDWAALS = -1070.0032 EELEC = -8050.0943 EGB = -1992.6928 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ A V E R A G E S O V E R 50 S T E P S NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 169.69 PRESS = 0.0 Etot = -4370.0542 EKtot = 840.8216 EPtot = -5210.8758 BOND = 229.1747 ANGLE = 616.0869 DIHED = 922.4572 1-4 NB = 424.1491 1-4 EEL = 3745.0528 VDWAALS = -1075.3383 EELEC = -8416.0952 EGB = -1656.3629 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 25.07 PRESS = 0.0 Etot = 33.7818 EKtot = 124.2085 EPtot = 124.3065 BOND = 34.3324 ANGLE = 77.8645 DIHED = 23.8847 1-4 NB = 16.6410 1-4 EEL = 26.8896 VDWAALS = 6.3944 EELEC = 226.2412 EGB = 199.9183 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.01 ( 0.03% of Total) | Calc gb radii 6.14 (17.07% of Gen B) | Calc gb diag 12.85 (35.75% of Gen B) | Calc gb off-diag 16.96 (47.17% of Gen B) | Gen Born time 35.95 (100.0% of Nonbo) | Nonbond force 35.95 (99.47% of Force) | Bond/Angle/Dihedral 0.19 ( 0.53% of Force) | Force time 36.15 (99.72% of Runmd) | Shake time 0.01 ( 0.02% of Runmd) | Verlet update time 0.09 ( 0.25% of Runmd) | Other 0.00 ( 0.01% of Runmd) | Runmd Time 36.25 (99.68% of Total) | Other 0.10 ( 0.29% of Total) | Total time 36.36 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 10:37:39.268 on 03/18/2010 | Setup done at 10:37:39.383 on 03/18/2010 | Run done at 10:38:15.629 on 03/18/2010 | wallclock() was called 1233 times