------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 09/28/2012 at 15:55:13 [-O]verwriting output File Assignments: | MDIN: stp1V0_l01.in | MDOUT: glaWAT_stp1V0_l01.out |INPCRD: glaWAT_stp0aV0_l01.rst | PARM: glaWAT.top |RESTRT: glaWAT_stp1V0_l01.rst | REFC: refc | MDVEL: mdvel | MDEN: glaWAT_stp1V0_l01.erg | MDCRD: glaWAT_stp1V0_l01.trj |MDINFO: glaWAT_stp1V0_l01.inf | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | Here is the input file: Step 1. NVT TI Thermal Equilibration in Water. SHAKE in solvent BUT not in solu &cntrl imin=0, nmropt=1, ntx=1, irest=0, ntrx=1, ntxo=1, ntpr=1000, ntwr=1000, iwrap=0, ntwx=1000, ntwv=0, ntwe=1000, ntf=2, ntc=2, ntb=1, ntp=0, igb=0, nsnb=25, cut=9.0, nstlim=300000, nscm=1000, nrespa=1, t=0.0, dt=0.001, vrand=0, vlimit=20.0, ig=18017, ntt=3, gamma_ln=2.0, temp0=298.0, tempi=0.0, tautp=0.5, tol=0.00001, icfe=1, clambda = 0.01, ifsc=1, scmask=':GLA@O1,HO1,H1', crgmask=':GLA', noshakemask=':GLA', / &wt type='TEMP0', istep1=0, istep2=100000, value1=0.0, value2=298.0, & &wt type='TEMP0', istep1=100001, istep2=300000, value1=298.0, value2=298.0, & &wt type='TAUTP', istep1=1, istep2=50000, value1=1.0, value2=4.0, & &wt type='TAUTP', istep1=50001, istep2=200000, value1=4.0, value2=2.0, & &wt type='TAUTP', istep1=200001, istep2=300000, value1=2.0, value2=1.0, & &wt type='END' / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MPI 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 = 14.990 | New format PARM file being parsed. | Version = 1.000 Date = 09/26/12 Time = 12:53:16 NATOM = 1872 NTYPES = 8 NBONH = 1860 MBONA = 12 NTHETH = 25 MTHETA = 17 NPHIH = 45 MPHIA = 33 NHPARM = 0 NPARM = 0 NNB = 2597 NRES = 617 NBONA = 12 NTHETA = 17 NPHIA = 33 NUMBND = 8 NUMANG = 13 NPTRA = 18 NATYP = 8 NPHB = 1 IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 179304 | Hollerith 6235 | Integer 64645 | Max Pairs 415272 | nblistReal 22464 | nblist Int 82156 | Total 3796 kbytes | Note: 1-4 EEL scale factors are being read from the topology file. | Note: 1-4 VDW scale factors are being read from the topology file. | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- default_name General flags: imin = 0, nmropt = 1 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 1000, ntrx = 1, ntwr = 1000 iwrap = 0, ntwx = 1000, ntwv = 0, ntwe = 1000 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 = 9.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 300000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 18017 temp0 = 298.00000, tempi = 0.00000, gamma_ln= 2.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 NMR refinement options: iscale = 0, noeskp = 1, ipnlty = 1, mxsub = 1 scalm = 100.00000, pencut = 0.10000, tausw = 0.10000 Free energy options: icfe = 1, ifsc = 1, klambda = 1 clambda = 0.0100, scalpha = 0.5000, scbeta = 12.0000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 31.399 Box Y = 29.981 Box Z = 31.561 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 32 NFFT2 = 30 NFFT3 = 32 Cutoff= 9.000 Tol =0.100E-04 Ewald Coefficient = 0.30768 Interpolation order = 4 | MPI Timing options: | profile_mpi = 0 Softcore potentials require ntf=1 because SHAKE constraints on some bonds might be removed *** input error(s)