:-) G R O M A C S (-: GROtesk MACabre and Sinister :-) VERSION 3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2004, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun_d (double precision) (-: Option Filename Type Description ------------------------------------------------------------ -s ethane_em.tpr Input Generic run input: tpr tpb tpa xml -o ethane_em.trr Output Full precision trajectory: trr trj -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -c ethane_em.gro Output Generic structure: gro g96 pdb xml -e ener.edr Output Generic energy: edr ene -g md.log Output Log file -dgdl dgdl.xvg Output, Opt. xvgr/xmgr file -field field.xvg Output, Opt. xvgr/xmgr file -table table.xvg Input, Opt. xvgr/xmgr file -tablep tablep.xvg Input, Opt. xvgr/xmgr file -rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -tpi tpi.xvg Output, Opt. xvgr/xmgr file -ei sam.edi Input, Opt. ED sampling input -eo sam.edo Output, Opt. ED sampling output -j wham.gct Input, Opt. General coupling stuff -jo bam.gct Output, Opt. General coupling stuff -ffout gct.xvg Output, Opt. xvgr/xmgr file -devout deviatie.xvg Output, Opt. xvgr/xmgr file -runav runaver.xvg Output, Opt. xvgr/xmgr file -pi pull.ppa Input, Opt. Pull parameters -po pullout.ppa Output, Opt. Pull parameters -pd pull.pdo Output, Opt. Pull data output -pn pull.ndx Input, Opt. Index file -mtx nm.mtx Output, Opt. Hessian matrix -dn dipole.ndx Output, Opt. Index file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -nice int 19 Set the nicelevel -deffnm string Set the default filename for all file options -[no]xvgr bool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -np int 1 Number of nodes, must be the same as used for grompp -nt int 1 Number of threads to start on each node -[no]v bool yes Be loud and noisy -[no]compact bool yes Write a compact log file -[no]sepdvdl bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -[no]multi bool no Do multiple simulations in parallel (only with -np > 1) -replex int 0 Attempt replica exchange every # steps -reseed int -1 Seed for replica exchange, -1 is generate a seed -[no]glas bool no Do glass simulation with special long range corrections -[no]ionize bool no Do a simulation including the effect of an X-Ray bombardment on your system Getting Loaded... Reading file ethane_em.tpr, VERSION 3.3 (double precision) Loaded with Money QM/MM calculation requested. Layer 0 nr of QM atoms 4 QMlevel: CPMD/STO-3G Number of atoms 8 Atom 1 C in residue 1 selected for QM-link atom with atom 0. Selected 5 atoms for QM calculation. QM bounding box: X: -0.3600 1.540 dx= 1.900 Y: -1.000 0.6300 dy= 1.630 Z: -0.7900 0.9400 dz= 1.730 QM simulation box:X: 0.000 9.525 dx= 9.525 Y: 0.000 9.525 dy= 9.525 Z: 0.000 9.525 dz= 9.525 Low-Memory BFGS Minimizer: Tolerance (Fmax) = 3.00000e+00 Number of steps = 1000 ------------------------------------------------------- Program mdrun_d, VERSION 3.3 Source code file: qm_cpmd.c, line: 935 Fatal error: execlp failed <./cpmdmpi> ! This usually happens if the QM ------------------------------------------------------- "Pump Up the Volume Along With the Tempo" (Jazzy Jeff) =========== GROMACS awaits QM-result for present step ==========