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【求助】gromacs的一个新问题
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版本问题算是解决了，但是又遇到一个新问题： zyj@zyj-laptop:~/桌面/drg$ grompp -f fullmd.mdp -c minimized_water.gro -p sys.to p -o fullmd.tpr :-) G R O M A C S (-: GROningen Mixture of Alchemy and Childrens' Stories :-) VERSION 4.0.7 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, 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. :-) grompp (-: Option Filename Type Description ------------------------------------------------------------ -f fullmd.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c minimized_water.gro Input Structure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -p sys.top Input Topology file -pp processed.top Output, Opt. Topology file -o fullmd.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -[no]v bool yes Be loud and noisy -time real -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int 0 Number of allowed warnings during input processing -[no]zero bool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... NOTE 1 [file fullmd.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. processing topology... Opening library file /usr/share/gromacs/top/ffG53a6.itp Opening library file /usr/share/gromacs/top/ffG53a6nb.itp Opening library file /usr/share/gromacs/top/ffG53a6bon.itp Opening library file /usr/share/gromacs/top/ff_dum.itp Generated 165 of the 1596 non-bonded parameter combinations Opening library file /usr/share/gromacs/top/spce.itp Opening library file /usr/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'DRG' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 290 K renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Analysing residue names: Opening library file /usr/share/gromacs/top/aminoacids.dat There are: 46055 OTHER residues There are: 0 PROTEIN residues There are: 0 DNA residues Analysing Other... ------------------------------------------------------- Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/readir.c, line: 1069 Fatal error: 137973 atoms are not part of any of the T-Coupling groups ------------------------------------------------------- "Look at these, my work-strong arms" (P.J. Harvey) |
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2楼2011-01-07 18:02:24
3楼2011-01-07 23:17:58
