------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | Run on 04/01/2010 at 12:04:32 [-O]verwriting output File Assignments: | MDIN: qmmm.in | MDOUT: FER-qmmm.out |INPCRD: FER-heat.rst | PARM: FER.prmtop |RESTRT: FER-qmmm.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: FER-qmmm.netcdf |MDINFO: FER-qmmm.mdinfo |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | Here is the input file: 300K constant temp QMMMMD &cntrl imin=0,irest=1,ntx=5, nstlim=100,dt=0.002, ntc=2,ntf=2, igb=5, ntb=0, cut=15, rgbmax=10, saltcon=0.300, nrespa=4, ntpr=1, ntwx=1, ntwr=1000, ioutfm=1, ntt=3, gamma_ln=2.0, temp0=300.0, ifqnt=1 / &qmmm qmmask=':1', qmcharge=2, spin=1, qmtheory=7, qmshake=0, qm_ewald=0, qm_pme=0, printcharges=1 / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MPI | New format PARM file being parsed. | Version = 1.000 Date = 04/01/10 Time = 11:48:11 NATOM = 1 NTYPES = 1 NBONH = 0 MBONA = 0 NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0 NHPARM = 0 NPARM = 0 NNB = 1 NRES = 1 NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 0 NUMANG = 0 NPTRA = 0 NATYP = 1 NPHB = 0 IFBOX = 0 NMXRS = 1 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are H(N)-modified Bondi radii (mbondi2) | Memory Use Allocated | Real 185 | Hollerith 9 | Integer 20018 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 79 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals LOADING THE QUANTUM ATOMS AS GROUPS Mask :1; matches 1 atoms -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- FER 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 = 1, ntrx = 1, ntwr = 1000 iwrap = 0, ntwx = 1, ntwv = 0, ntwe = 0 ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 0, igb = 5, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 15.00000, intdiel = 1.00000 saltcon = 0.30000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00500 rdt = 0.00000, rgbmax = 10.00000 extdiel = 78.50000 alpb = 0 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 100, nscm = 1000, nrespa = 4 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 71277 temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 QMMM options: ifqnt = True nquant = 1 qmgb = 2 qmcharge = 2 adjust_q = 2 spin = 1 qmcut = 15.0000 qmshake = 0 lnk_atomic_no = 1 lnk_dis = 1.0900 qmmm_int = 1 qm_theory = DFTB verbosity = 0 qmqmdx = Analytical tight_p_conv = False (converge density to 0.05xSqrt[SCFCRT]) scfconv = 0.100E-07 itrmax = 1000 printcharges = True peptide_corr = False qmqmrij_incore = False qmmmrij_incore = False qmqm_erep_incore = False pseudo_diag = False diag_routine = 1 qm_ewald = 0 qm_pme = False | MPI Timing options: | profile_mpi = 0 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- FER begin time read from input coords = 20.000 ps Number of triangulated 3-point waters found: 0 | Atom division among processors: | 0 1 |QMMM: Running QMMM calculation in parallel mode on 1 threads. |QMMM: All atom division among threads: |QMMM: Start End Count |QMMM: Thread( 0): 1-> 1 ( 1) |QMMM: Quantum atom + link atom division among threads: |QMMM: Start End Count |QMMM: Thread( 0): 1-> 1 ( 1) | Running AMBER/MPI version on 1 nodes | # of SOLUTE degrees of freedom (RNDFP): 3. | # of SOLVENT degrees of freedom (RNDFS): 0. | NDFMIN = 3. NUM_NOSHAKE = 0 CORRECTED RNDFP = 3. | TOTAL # of degrees of freedom (RNDF) = 3. QMMM: Link Atom Information QMMM: ------------------------------------------------------------------------ QMMM: nlink = 0 QMMM: ------------------------------------------------------------------------ -------------------------------------------------------------------------------- 3.1 QM CALCULATION INFO -------------------------------------------------------------------------------- n_atomic_orb of 9 exceeds max_valence_orbitals of MAX_VALENCE_ORBITALS SANDER BOMB in subroutine qm2_load_params.f exceeded max Check qmmm_module.f and parameters.h