------------------------------------------------------- Amber 7 SANDER Scripps/UCSF 2002 ------------------------------------------------------- | Sun May 31 22:09:19 2009 File Assignments: | MDIN: mdin | MDOUT: mdout |INPCRD: methane.crd | PARM: methane.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=5, 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 = 22:09:19 NATOM = 5 NTYPES = 2 NBONH = 4 MBONA = 0 NTHETH = 6 MTHETA = 0 NPHIH = 0 MPHIA = 0 NHPARM = 0 NPARM = 0 NNB = 11 NRES = 1 NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 1 NUMANG = 1 NPTRA = 0 NATYP = 2 NPHB = 0 IFBOX = 0 NMXRS = 5 IFCAP = 0 NEXTRA = 0 | Memory Use Allocated Used | Real 2000000 1416 | Hollerith 400000 33 | Integer 2000000 350861 | 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 = 5, 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 3.027 2.454 0. FORCE 0 0.0150052262 -1.509897E-13 0. FORCE 1 -0.498780107 0.27971467 1.81921501E-18 FORCE 2 0.0989107589 -0.145037419 -0.147955616 FORCE 3 0.0989107589 -0.145037419 0.147955616 FORCE 4 0.285953363 0.0103601683 -1.16890547E-18 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = 0.0003 EKtot = 0.0000 EPtot = 0.0003 BOND = 0.0001 ANGLE = 0.0001 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 ------------------------------------------------------------------------------ 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 3.027 2.454 0. FORCE 0 0.0150052262 -1.509897E-13 0. FORCE 1 -0.498780107 0.27971467 1.81921501E-18 FORCE 2 0.0989107589 -0.145037419 -0.147955616 FORCE 3 0.0989107589 -0.145037419 0.147955616 FORCE 4 0.285953363 0.0103601683 -1.16890547E-18 NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0 Etot = 0.0003 EKtot = 0.0000 EPtot = 0.0003 BOND = 0.0001 ANGLE = 0.0001 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 ------------------------------------------------------------------------------ COORD 0 2.00000311 1. 0. COORD 1 1.99999131 2.09000487 3.16891066E-23 COORD 2 1.48602053 2.4539699 0.889969293 COORD 3 1.48602053 2.4539699 -0.889969293 COORD 4 3.02705935 2.45400215 -2.42598343E-22 FORCE 0 0.0136031113 0.00331340958 -4.31365968E-24 FORCE 1 -0.422214453 0.260735719 -1.81262871E-17 FORCE 2 0.0820898436 -0.131436353 -0.121153313 FORCE 3 0.0820898436 -0.131436353 0.121153313 FORCE 4 0.244431654 -0.0011764229 1.59242007E-18 NSTEP = 2 TIME(PS) = 0.002 TEMP(K) = 0.00 PRESS = 0.0 Etot = 0.0003 EKtot = 0.0000 EPtot = 0.0002 BOND = 0.0001 ANGLE = 0.0001 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 ------------------------------------------------------------------------------ COORD 0 2.00001187 1.00000138 -1.79054118E-27 COORD 1 1.99996791 2.09001883 -5.6810937E-22 COORD 2 1.48607513 2.45388524 0.889888297 COORD 3 1.48607513 2.45388524 -0.889888297 COORD 4 3.02722016 2.45400381 1.75795125E-22 FORCE 0 0.00978182737 0.0118690228 8.49646761E-24 FORCE 1 -0.216530005 0.208313281 6.11224223E-19 FORCE 2 0.0369342352 -0.0943338715 -0.0492777504 FORCE 3 0.0369342352 -0.0943338715 0.0492777504 FORCE 4 0.132879707 -0.0315145603 1.17568916E-18 NSTEP = 3 TIME(PS) = 0.003 TEMP(K) = 0.01 PRESS = 0.0 Etot = 0.0003 EKtot = 0.0001 EPtot = 0.0001 BOND = 0.0000 ANGLE = 0.0001 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 ------------------------------------------------------------------------------ COORD 0 2.0000247 1.00000768 -5.43147747E-29 COORD 1 1.99993697 2.09004004 -1.14661388E-21 COORD 2 1.48614506 2.45376142 0.889786846 COORD 3 1.48614506 2.45376142 -0.889786846 COORD 4 3.02743612 2.45399239 1.0822011E-21 FORCE 0 0.00457821877 0.0220104054 2.55533678E-25 FORCE 1 0.0537977697 0.134653414 5.52773657E-18 FORCE 2 -0.0222896315 -0.0437113487 0.0447361248 FORCE 3 -0.0222896315 -0.0437113487 -0.0447361248 FORCE 4 -0.0137967255 -0.0692411221 1.58225773E-18 NSTEP = 4 TIME(PS) = 0.004 TEMP(K) = 0.02 PRESS = 0.0 Etot = 0.0003 EKtot = 0.0002 EPtot = 0.0001 BOND = 0.0000 ANGLE = 0.0001 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 ------------------------------------------------------------------------------ COORD 0 2.00003942 1.00002312 1.78798017E-27 COORD 1 1.99990791 2.09006595 -1.53254189E-21 COORD 2 1.48620575 2.45361946 0.889703964 COORD 3 1.48620575 2.45361946 -0.889703964 COORD 4 3.02764636 2.45395223 2.64538063E-21 FORCE 0 -0.000636770156 0.0291298751 -4.95193525E-23 FORCE 1 0.304131566 0.0560577559 -7.39705831E-18 FORCE 2 -0.0768041343 0.00718340956 0.130701325 FORCE 3 -0.0768041343 0.00718340956 -0.130701325 FORCE 4 -0.149886527 -0.0995544501 3.33389078E-18 NSTEP = 5 TIME(PS) = 0.005 TEMP(K) = 0.01 PRESS = 0.0 Etot = 0.0003 EKtot = 0.0001 EPtot = 0.0001 BOND = 0.0001 ANGLE = 0.0001 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 ------------------------------------------------------------------------------ A V E R A G E S O V E R 5 S T E P S NSTEP = 5 TIME(PS) = 0.005 TEMP(K) = 0.01 PRESS = 0.0 Etot = 0.0003 EKtot = 0.0001 EPtot = 0.0002 BOND = 0.0001 ANGLE = 0.0001 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 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 5 TIME(PS) = 0.005 TEMP(K) = 0.01 PRESS = 0.0 Etot = 0.0000 EKtot = 0.0001 EPtot = 0.0001 BOND = 0.0000 ANGLE = 0.0000 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) = -1.66 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Highest rstack allocated: 0 | Highest istack allocated: 192 | Setup wallclock 0 seconds | Nonsetup wallclock 0 seconds