------------------------------------------------------- Amber 7 SANDER Scripps/UCSF 2002 ------------------------------------------------------- | Sun May 31 22:11:09 2009 File Assignments: | MDIN: mdin | MDOUT: mdout |INPCRD: peptide.crd | PARM: peptide.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 = 22:11:09 NATOM = 12 NTYPES = 7 NBONH = 7 MBONA = 4 NTHETH = 14 MTHETA = 4 NPHIH = 16 MPHIA = 3 NHPARM = 0 NPARM = 0 NNB = 46 NRES = 2 NBONA = 4 NTHETA = 4 NPHIA = 3 NUMBND = 7 NUMANG = 10 NPTRA = 5 NATYP = 7 NPHB = 0 IFBOX = 0 NMXRS = 6 IFCAP = 0 NEXTRA = 0 | Memory Use Allocated Used | Real 2000000 1920 | Hollerith 400000 76 | Integer 2000000 386564 | 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 = 21 | TOTAL SIZE OF NONBOND LIST = 21 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 3.427 2.641 0. COORD 5 4.391 1.877 0. COORD 6 3.555 3.97 0. COORD 7 2.733 4.556 0. COORD 8 4.853 4.614 0. COORD 9 5.636 3.855 0. COORD 10 4.951 5.236 -0.89 COORD 11 4.951 5.236 0.89 FORCE 0 4.24224032 0.682679742 4.33680869E-19 FORCE 1 4.89526984 10.4050636 -3.76457441E-17 FORCE 2 0.571590324 -1.91164955 -0.805035097 FORCE 3 0.571590324 -1.91164955 0.805035097 FORCE 4 -7.83880415 -9.52554008 2.96529294E-17 FORCE 5 -10.2821108 -2.76044236 7.15573434E-17 FORCE 6 -1.63453044 -2.56400412 -2.08166817E-17 FORCE 7 -0.542003385 -4.63459634 -1.0489656E-17 FORCE 8 1.91626545 8.32937303 -9.90350922E-18 FORCE 9 5.27050141 3.88693462 0. FORCE 10 1.41499553 0.00191549095 -0.360174932 FORCE 11 1.41499553 0.00191549095 0.360174932 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -29.5524 EKtot = 0.0000 EPtot = -29.5524 BOND = 0.0196 ANGLE = 0.0630 DIHED = 0.0000 1-4 NB = 1.3117 1-4 EEL = -18.5367 VDWAALS = 0.6139 EELEC = -13.0240 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 3.427 2.641 0. COORD 5 4.391 1.877 0. COORD 6 3.555 3.97 0. COORD 7 2.733 4.556 0. COORD 8 4.853 4.614 0. COORD 9 5.636 3.855 0. COORD 10 4.951 5.236 -0.89 COORD 11 4.951 5.236 0.89 FORCE 0 4.24224032 0.682679742 4.33680869E-19 FORCE 1 4.89526984 10.4050636 -3.76457441E-17 FORCE 2 0.571590324 -1.91164955 -0.805035097 FORCE 3 0.571590324 -1.91164955 0.805035097 FORCE 4 -7.83880415 -9.52554008 2.96529294E-17 FORCE 5 -10.2821108 -2.76044236 7.15573434E-17 FORCE 6 -1.63453044 -2.56400412 -2.08166817E-17 FORCE 7 -0.542003385 -4.63459634 -1.0489656E-17 FORCE 8 1.91626545 8.32937303 -9.90350922E-18 FORCE 9 5.27050141 3.88693462 0. FORCE 10 1.41499553 0.00191549095 -0.360174932 FORCE 11 1.41499553 0.00191549095 0.360174932 NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0 Etot = -29.5524 EKtot = 0.0000 EPtot = -29.5524 BOND = 0.0196 ANGLE = 0.0630 DIHED = 0.0000 1-4 NB = 1.3117 1-4 EEL = -18.5367 VDWAALS = 0.6139 EELEC = -13.0240 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ COORD 0 2.00088045 1.00014169 9.00075011E-23 COORD 1 2.00008527 2.09018125 -6.55755361E-22 COORD 2 1.48611863 2.45360325 0.88983292 COORD 3 1.48611863 2.45360325 -0.88983292 COORD 4 3.42686346 2.64083407 5.16527643E-22 COORD 5 4.39086556 1.87696391 9.35627974E-22 COORD 6 3.55497559 3.96996171 -3.10843892E-22 COORD 7 2.73288751 4.55503812 -2.17705643E-21 COORD 8 4.85303338 4.61414509 -1.72510318E-22 COORD 9 5.63709386 3.85580671 0. COORD 10 4.95129367 5.2360004 -0.890074752 COORD 11 4.95129367 5.2360004 0.890074752 FORCE 0 4.16096053 0.709724989 -1.7320105E-18 FORCE 1 5.01469465 9.97385577 -5.42171467E-17 FORCE 2 0.473412082 -1.80114328 -0.619981359 FORCE 3 0.473412082 -1.80114328 0.619981359 FORCE 4 -7.63150886 -9.10661619 -3.10270606E-17 FORCE 5 -10.2172716 -2.81073494 5.24432248E-19 FORCE 6 -1.32198391 -3.02805253 1.38735423E-17 FORCE 7 -0.81356652 -4.32942545 -2.40504348E-17 FORCE 8 2.17040612 8.24214649 8.71022555E-18 FORCE 9 4.98101657 3.87799564 -4.45186036E-24 FORCE 10 1.35521442 0.0366963959 -0.340275086 FORCE 11 1.35521442 0.0366963959 0.340275086 NSTEP = 2 TIME(PS) = 0.002 TEMP(K) = 0.90 PRESS = 0.0 Etot = -29.5529 EKtot = 0.0269 EPtot = -29.5798 BOND = 0.0184 ANGLE = 0.0598 DIHED = 0.0000 1-4 NB = 1.3091 1-4 EEL = -18.5574 VDWAALS = 0.6062 EELEC = -13.0160 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) = 0.45 PRESS = 0.0 Etot = -29.5527 EKtot = 0.0134 EPtot = -29.5661 BOND = 0.0190 ANGLE = 0.0614 DIHED = 0.0000 1-4 NB = 1.3104 1-4 EEL = -18.5470 VDWAALS = 0.6101 EELEC = -13.0200 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) = 0.45 PRESS = 0.0 Etot = 0.0002 EKtot = 0.0134 EPtot = 0.0137 BOND = 0.0006 ANGLE = 0.0016 DIHED = 0.0000 1-4 NB = 0.0013 1-4 EEL = 0.0104 VDWAALS = 0.0039 EELEC = 0.0040 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ | Zhou-Berne energy conservation: log10(DeltaE) = -5.08 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Highest rstack allocated: 25 | Highest istack allocated: 566 | Setup wallclock 0 seconds | Nonsetup wallclock 0 seconds