------------------------------------------------------- Amber 7 SANDER Scripps/UCSF 2002 ------------------------------------------------------- | Sun May 31 22:07:10 2009 File Assignments: | MDIN: mdin | MDOUT: mdout |INPCRD: methanol.crd | PARM: methanol.top |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Simple MD &cntrl imin=0, ntx=1, dt=0.001 cut=1000, ntt=0, temp0=0.0, ntb=0, nstlim=2, ntwe=1, ntwx=1, ntpr=1, &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation | *** cutoff > system size, list only builds once | New format PARM file being parsed. | Version = 1.000 Date = 05/31/09 Time = 22:07:10 NATOM = 6 NTYPES = 4 NBONH = 4 MBONA = 1 NTHETH = 7 MTHETA = 0 NPHIH = 3 MPHIA = 0 NHPARM = 0 NPARM = 0 NNB = 16 NRES = 1 NBONA = 1 NTHETA = 0 NPHIA = 0 NUMBND = 3 NUMANG = 3 NPTRA = 1 NATYP = 4 NPHB = 0 IFBOX = 0 NMXRS = 6 IFCAP = 0 NEXTRA = 0 | Memory Use Allocated Used | Real 2000000 1497 | Hollerith 400000 39 | Integer 2000000 350984 | Max Nonbonded Pairs: 5400000 | 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 = 1, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 1, ntwv = 0, ntwe = 1 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 0, nsnb = 25 ipol = 0, gbsa = 0 dielc = 1.00000, cut =1000.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 2, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 20.00000 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 Sum of charges from parm topology file = 0.00000000 Forcing neutrality... -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- eedmeth=4: Setting switch to one everywhere --------------------------------------------------- | Local SIZE OF NONBOND LIST = 0 | TOTAL SIZE OF NONBOND LIST = 0 COORD 0 2. 1. 0. COORD 1 2. 2.09 0. COORD 2 1.486 2.454 0.89 COORD 3 1.486 2.454 -0.89 COORD 4 3.348 2.566 0. COORD 5 3.348 3.526 0. FORCE 0 -0.192141943 -0.201546122 0. FORCE 1 11.2430258 5.61314917 8.87636319E-16 FORCE 2 -0.157710113 -0.293564152 -0.00805898386 FORCE 3 -0.157710113 -0.293564152 0.00805898386 FORCE 4 -9.49989169 -5.34525971 -1.52547246E-15 FORCE 5 -1.23557195 0.520784971 1.14144805E-15 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = 2.4025 EKtot = 0.0000 EPtot = 2.4025 BOND = 0.1227 ANGLE = 0.0152 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 2.2647 VDWAALS = 0.0000 EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ COORD 0 2. 1. 0. COORD 1 2. 2.09 0. COORD 2 1.486 2.454 0.89 COORD 3 1.486 2.454 -0.89 COORD 4 3.348 2.566 0. COORD 5 3.348 3.526 0. FORCE 0 -0.192141943 -0.201546122 0. FORCE 1 11.2430258 5.61314917 8.87636319E-16 FORCE 2 -0.157710113 -0.293564152 -0.00805898386 FORCE 3 -0.157710113 -0.293564152 0.00805898386 FORCE 4 -9.49989169 -5.34525971 -1.52547246E-15 FORCE 5 -1.23557195 0.520784971 1.14144805E-15 NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0 Etot = 2.4025 EKtot = 0.0000 EPtot = 2.4025 BOND = 0.1227 ANGLE = 0.0152 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 2.2647 VDWAALS = 0.0000 EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ COORD 0 1.99996012 0.99995817 0. COORD 1 2.00019584 2.09009778 1.54618348E-20 COORD 2 1.48596727 2.45393907 0.889998327 COORD 3 1.48596727 2.45393907 -0.889998327 COORD 4 3.34787579 2.56593011 -1.99458873E-20 COORD 5 3.34774357 3.52610809 2.36899743E-19 FORCE 0 -0.1575754 -0.106591732 -1.28622708E-19 FORCE 1 10.9064679 5.39997081 8.89989637E-16 FORCE 2 -0.111385378 -0.281686771 -0.0306770016 FORCE 3 -0.111385378 -0.281686771 0.0306770016 FORCE 4 -9.31082057 -5.05377851 -1.52575784E-15 FORCE 5 -1.21530117 0.323772974 1.13674606E-15 NSTEP = 2 TIME(PS) = 0.002 TEMP(K) = 0.38 PRESS = 0.0 Etot = 2.4025 EKtot = 0.0046 EPtot = 2.3979 BOND = 0.1183 ANGLE = 0.0149 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 2.2647 VDWAALS = 0.0000 EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ A V E R A G E S O V E R 2 S T E P S NSTEP = 2 TIME(PS) = 0.002 TEMP(K) = 0.19 PRESS = 0.0 Etot = 2.4025 EKtot = 0.0023 EPtot = 2.4002 BOND = 0.1205 ANGLE = 0.0150 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 2.2647 VDWAALS = 0.0000 EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 2 TIME(PS) = 0.002 TEMP(K) = 0.19 PRESS = 0.0 Etot = 0.0000 EKtot = 0.0023 EPtot = 0.0023 BOND = 0.0022 ANGLE = 0.0002 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000 EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ | Zhou-Berne energy conservation: log10(DeltaE) = -4.78 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Highest rstack allocated: 0 | Highest istack allocated: 242 | Setup wallclock 0 seconds | Nonsetup wallclock 0 seconds