------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | Run on 10/13/2009 at 14:19:45 [-O]verwriting output File Assignments: | MDIN: /home/ba01/u117/rchaud5/amber10/md_nve2les.in | MDOUT: md_nve7_plp617_les.out |INPCRD: /home/ba01/u117/rchaud5/amber10/les.crd | PARM: /home/ba01/u117/rchaud5/amber10/les.prmtop |RESTRT: md_nve7_plp617_les.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: md_nve7_plp617_les.x |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | Here is the input file: density equilibration w restraints &cntrl imin = 0, ipimd = 2, ntx = 5, irest = 1, ntpr = 2500, ntwr = 2500, ntwx = 2500, tol=0.000001, ntf = 2, ntb = 1, cut = 10.0, nstlim = 1000000, dt = 0.002, nrespa=2, temp0 = 300.0, ntt = 4, temp0les = -1, tautp = 5.0, ntc = 2, nchain = 4, ntp = 0, pres0 = 1.0, comp = 44.6, taup = 2.0, iwrap = 1, &end &ewald dsum_tol = 0.000001, &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MPI USE_MPI_IN_PLACE LES 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 = 30.763 NATOM = 43662 NTYPES = 30 NBONH = 31730 MBONA = 11981 NTHETH = 4388 MTHETA = 2794 NPHIH = 8573 MPHIA = 5380 NHPARM = 0 NPARM = 1 NNB = 130935 NRES = 10169 NBONA = 11981 NTHETA = 2794 NPHIA = 5380 NUMBND = 61 NUMANG = 122 NPTRA = 62 NATYP = 33 NPHB = 1 IFBOX = 2 NMXRS = 105 IFCAP = 0 NEXTRA = 9929 NCOPY = 5 | Memory Use Allocated | Real 2322905 | Hollerith 272143 | Integer 1493196 | Max Pairs 3772396 | nblistReal 523944 | nblist Int 1507679 | Total 49762 kbytes LES parameters were found 0 LES atom pairs require adjustment | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 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 = 2500, ntrx = 1, ntwr = 2500 iwrap = 1, ntwx = 2500, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 1, 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 = 1000000, nscm = 1000001, nrespa = 2 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Nose-Hoover chains gamma_ln= 0.00000 number of oscillators= 4 SHAKE: ntc = 2, jfastw = 0 tol = 0.00000 Extra-points options: frameon = 1, chngmask= 1 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 75.353 Box Y = 75.353 Box Z = 75.353 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 80 NFFT2 = 75 NFFT3 = 75 Cutoff= 10.000 Tol =0.100E-05 Ewald Coefficient = 0.31234 Interpolation order = 4 | MPI Timing options: | profile_mpi = 0 LES requires numextra=0