------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | Run on 07/23/2010 at 17:52:02 [-O]verwriting output File Assignments: | MDIN: md1.in | MDOUT: mgomespc_md1.out |INPCRD: mgomespc_md.rst | PARM: mgomespc.top |RESTRT: mgomespc_md1.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mgomespc_md1.mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | Here is the input file: 5gal MD in water TIP3P, for Constant valume and temp., Nose-Hoover thermostat &cntrl imin = 0, ipimd = 2, ntx = 5, irest = 1, ntpr = 2000, ntwr = 2000, ntwx = 4000, tol=0.000001, ntf = 2, ntb = 2, cut = 10.0, dt = 0.002, nstlim = 500000, nrespa = 1, temp0 = 288.0, ntt = 4, temp0les = -1, tautp = 5.0, ntc = 2, nchain = 4, ntp = 1, pres0 = 1.0, comp = 44.6, taup = 2.0, iwrap = 1, &end / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MPI USE_MPI_IN_PLACE getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read | peek_ewald_inpcrd: Box info found |Largest sphere to fit in unit cell has radius = 17.130 | New format PARM file being parsed. | Version = 1.000 Date = 07/19/10 Time = 12:07:31 NATOM = 2805 NTYPES = 8 NBONH = 2781 MBONA = 25 NTHETH = 53 MTHETA = 36 NPHIH = 89 MPHIA = 72 NHPARM = 0 NPARM = 0 NNB = 3946 NRES = 922 NBONA = 25 NTHETA = 36 NPHIA = 72 NUMBND = 8 NUMANG = 12 NPTRA = 18 NATYP = 8 NPHB = 1 IFBOX = 1 NMXRS = 22 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 226374 | Hollerith 17754 | Integer 84185 | Max Pairs 107712 | nblistReal 33660 | nblist Int 94757 | Total 3220 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 5, irest = 1, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 2000, ntrx = 1, ntwr = 2000 iwrap = 1, ntwx = 4000, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 2, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 10.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 500000, nscm = 500001, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Nose-Hoover chains gamma_ln= 0.00000 number of oscillators= 4 Pressure regulation: ntp = 1 pres0 = 1.00000, comp = 44.60000, taup = 2.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 34.986 Box Y = 34.260 Box Z = 35.643 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 | MPI Timing options: | profile_mpi = 0 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 40.000 ps Number of triangulated 3-point waters found: 919 | Atom division among processors: | 0 141 282 423 564 705 846 987 | 1128 1269 1410 1551 1692 1833 1971 2112 | 2250 2388 2529 2667 2805 Sum of charges from parm topology file = -0.00000101 Forcing neutrality... | Running AMBER/MPI version on 20 nodes | WARNING: The number of processors is not a power of 2 | this may be inefficient on some systems. -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- THIS IS A NORMAL-MODE PIMD RUN Parameters: number of beads = 1 number of classical atoms = 2805 temperature (Kelvin) = 288.00 | # of SOLUTE degrees of freedom (RNDFP): 5634. | # of SOLVENT degrees of freedom (RNDFS): 0. | NDFMIN = 5634. NUM_NOSHAKE = 0 CORRECTED RNDFP = 5634. | TOTAL # of degrees of freedom (RNDF) = 5634.