------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | Run on 07/21/2008 at 01:01:13 [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: poh.out |INPCRD: poh.crd | PARM: poh.top |RESTRT: poh.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | Here is the input file: POH: EVB MD in the NVT ensemble &cntrl imin = 0, ievb = 1, irest = 1, ntx = 7, ntb = 0, cut = 9999.0, tempi = 300.0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0, nstlim = 20, dt = 0.0005, nscm = 10000, ntpr = 1, ntwx = 2000, ntwr = 2000 / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MPI USE_MPI_IN_PLACE | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation | *** cutoff > system size, list only builds once |Largest sphere to fit in unit cell has radius = 31.509 | New format PARM file being parsed. | Version = 1.000 Date = 01/11/07 Time = 14:45:07 NATOM = 12 NTYPES = 6 NBONH = 5 MBONA = 7 NTHETH = 9 MTHETA = 8 NPHIH = 18 MPHIA = 9 NHPARM = 0 NPARM = 0 NNB = 50 NRES = 1 NBONA = 7 NTHETA = 8 NPHIA = 9 NUMBND = 6 NUMANG = 9 NPTRA = 4 NATYP = 6 NPHB = 0 IFBOX = 0 NMXRS = 12 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 1790 | Hollerith 75 | Integer 20863 | Max Pairs 66 | nblistReal 144 | nblist Int 881954 | Total 3542 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- HP General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 7, irest = 1, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 2000 iwrap = 0, ntwx = 2000, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut =9999.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 20, nscm = 10000, nrespa = 1 t = 0.00000, dt = 0.00050, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 71277 temp0 = 300.00000, tempi = 300.00000, gamma_ln= 1.00000 | MPI Timing options: | profile_mpi = 0 Reading EVB input file from poh.evb_template_L_0_S2 No. of DG at TS = 1 No. of DG at minima = 2 No. of additional DG = 6 Total DG points = 9 EVB options: nevb = 2, nbias = 1, nmorse = 0, ntw_evb = 1 xch_type = dist_gauss evb_dyn = dbonds_umb dia_shift( 1) = 0.00000 dia_shift( 2) = 0.00000 dbonds_umb( 7, 8, 1) :: k = 800.00000 ezero= 0.00000 No. of redundant internal bonds = 13 No. of redundant internal angles = 19 No. of redundant internal dihedrals = 24 No. of internal coordinates = 56 DG:: Opening file: 2hydroxypyridine_56.fchk DG:: Opening file: pyridone_56.fchk DG:: Opening file: 2hydroxypyridine_TS_56_vtight.fchk DG:: Opening file: 2hydroxypyridine_TS_56_vtight.fchk DG:: Opening file: 2hydroxypyridine_56.fchk DG:: Opening file: pyridone_56.fchk DG:: Opening file: onehalfR_56.fchk DG:: Opening file: onehalfP_56.fchk DG:: Opening file: irc_plusonehalf_56.fchk DG:: Opening file: irc_minusonehalf_56.fchk DG:: Opening file: irc_plusonefourth_56.fchk DG:: Opening file: irc_minusonefourth_56.fchk | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- HP begin time read from input coords = 925.000 ps Number of triangulated 3-point waters found: 0 | Atom division among processors: | 0 12 | EVB data will be written to evbout DG:: external file name and associated alpha exponent 1 2hydroxypyridine_TS_56_vtight.fchk 17.56920 2 2hydroxypyridine_56.fchk 10.68790 3 pyridone_56.fchk 10.68790 4 onehalfR_56.fchk 7.32050 5 onehalfP_56.fchk 7.32050 6 irc_plusonehalf_56.fchk 11.71280 7 irc_minusonehalf_56.fchk 11.71280 8 irc_plusonefourth_56.fchk 12.88410 9 irc_minusonefourth_56.fchk 12.88410 DG:: subspace = no_dihedrals DG:: nselect = 32 DG:: scoord(:) = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 DG:: No. of DG ab initio configuration points = 9 DG:: No. of DG data points within each configuration point = 561 DG:: nUFF_D = 1 1 8 3