------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | Run on 12/08/2009 at 15:33:31 [-O]verwriting output File Assignments: | MDIN: mdin_min_v1_l1 | MDOUT: plm_min_v1_l1.out |INPCRD: plm.rst | PARM: plm.prm |RESTRT: plm_min_v1_l1.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | Here is the input file: density minlibration &cntrl imin = 1, ntx = 1, ntmin = 2, maxcyc=500, ntpr = 100, ntf = 1, ntc = 2, ntb = 1, cut = 9.0, icfe=1, clambda = 0.1, ifsc=1, crgmask=':PLM@C15,H28,H29,C16,H30,H31,H32', scmask=':PLM@C15,H28,H29,C16,H30,H31,H32', &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 = 15.674 | New format PARM file being parsed. | Version = 1.000 Date = 12/08/09 Time = 15:24:56 NATOM = 3635 NTYPES = 7 NBONH = 3616 MBONA = 17 NTHETH = 76 MTHETA = 17 NPHIH = 121 MPHIA = 40 NHPARM = 0 NPARM = 0 NNB = 5055 NRES = 1197 NBONA = 17 NTHETA = 17 NPHIA = 40 NUMBND = 6 NUMANG = 7 NPTRA = 10 NATYP = 7 NPHB = 1 IFBOX = 1 NMXRS = 49 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 313109 | Hollerith 23009 | Integer 102165 | Max Pairs 1612728 | nblistReal 43620 | nblist Int 164857 | Total 10219 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 1, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 100, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 9.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 500, ncyc = 10, ntmin = 2 dx0 = 0.01000, drms = 0.00010 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 Free energy options: icfe = 1, ifsc = 1 klambda = 1 clambda = 0.10000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 0 Box X = 51.041 Box Y = 32.863 Box Z = 31.349 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 54 NFFT2 = 32 NFFT3 = 32 Cutoff= 9.000 Tol =0.100E-04 Ewald Coefficient = 0.30768 Interpolation order = 4 | MPI Timing options: | profile_mpi = 0 Zero-Charge Mask :PLM@C15,H28,H29,C16,H30,H31,H32; matches 7 atoms Removing charge of -0.2356 from atom 1 Removing charge of 0.0520 from atom 2 Removing charge of 0.0520 from atom 3 Removing charge of 0.0520 from atom 4 Removing charge of 0.1452 from atom 5 Removing charge of -0.0235 from atom 6 Removing charge of -0.0235 from atom 7 Total charge of 0.0187 removed -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 1195 | Atom division among processors: | 0 3635 Softcore Mask :PLM@C15,H28,H29,C16,H30,H31,H32; matches 7 atoms this run corresponds to V1, its softcore atoms interact fully for lambda=1 this process: 3635 atoms, partner process: 3629 atoms Checking for mismatched coordinates. WARNING: Local coordinate 22 differs from partner coordinate 1 ! SANDER BOMB in subroutine sc_check_and_adjust Atom coordinate disagreement Check input files.