[gmx-users] Gromac4 grompp -v Err
Tsjerk Wassenaar
tsjerkw at gmail.com
Tue Mar 10 10:09:13 CET 2009
Hi Li Bei,
You're using an old .mdp parameter file. Use a new one. If you make an
empty .mdp file (touch empty.mdp) and use it as input to grompp, a
.mdp file with all parameters set to default will be generated
(mdout.mdp).
Cheers,
Tsjerk
On Tue, Mar 10, 2009 at 9:59 AM, li bai <javacfish at yahoo.com.cn> wrote:
> Hello,everyone!
> I have install gromacs4, but when I stury the tutor of gromacs, and input
> command "grompp -v in every examples", the err be engenderred as below:
>
> li at localhost water]$ grompp -v
> :-) G R O M A C S (-:
>
> Go Rough, Oppose Many Angry Chinese Serial killers
>
> :-) VERSION 4.0.4 (-:
>
>
> 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 grompp.mdp Input, Opt. grompp input file with MD parameters
> -po mdout.mdp Output grompp input file with MD parameters
> -c conf.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 topol.top Input Topology file
> -pp processed.top Output, Opt. Topology file
> -o topol.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'
> Ignoring obsolete mdp entry 'domain-decomposition'
> Replacing old mdp entry 'unconstrained-start' by 'continuation'
> Ignoring obsolete mdp entry 'dihre-tau'
> Ignoring obsolete mdp entry 'nstdihreout'
> Ignoring obsolete mdp entry 'nstcheckpoint'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
>
> WARNING 1 [file grompp.mdp, line unknown]:
> Unknown or double left-hand 'bd-temp' in parameter file
>
>
> checking input for internal consistency...
>
> NOTE 1 [file grompp.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 /home/bai/workdir/gromacs4/share/gromacs/top/ffgmx.itp
> Opening library file
> /home/bai/workdir/gromacs4/share/gromacs/top/ffgmxnb.itp
> Opening library file
> /home/bai/workdir/gromacs4/share/gromacs/top/ffgmxbon.itp
> Opening library file /home/bai/workdir/gromacs4/share/gromacs/top/ff_dum.itp
> Opening library file /home/bai/workdir/gromacs4/share/gromacs/top/spc.itp
> Generated 1284 of the 1485 non-bonded parameter combinations
> Excluding 2 bonded neighbours molecule type 'SOL'
> processing coordinates...
> double-checking input for internal consistency...
> Velocities were taken from a Maxwell distribution at 300 K
> renumbering atomtypes...
> converting bonded parameters...
> initialising group options...
> processing index file...
> Analysing residue names:
> Opening library file
> /home/bai/workdir/gromacs4/share/gromacs/top/aminoacids.dat
> There are: 216 OTHER residues
> There are: 0 PROTEIN residues
> There are: 0 DNA residues
> Analysing Other...
> Making dummy/rest group for Acceleration containing 648 elements
> Making dummy/rest group for Freeze containing 648 elements
> Making dummy/rest group for Energy Mon. containing 648 elements
> Making dummy/rest group for VCM containing 648 elements
> Number of degrees of freedom in T-Coupling group System is 1293.00
> Making dummy/rest group for User1 containing 648 elements
> Making dummy/rest group for User2 containing 648 elements
> Making dummy/rest group for XTC containing 648 elements
> Making dummy/rest group for Or. Res. Fit containing 648 elements
> Making dummy/rest group for QMMM containing 648 elements
> T-Coupling has 1 element(s): System
> Energy Mon. has 1 element(s): rest
> Acceleration has 1 element(s): rest
> Freeze has 1 element(s): rest
> User1 has 1 element(s): rest
> User2 has 1 element(s): rest
> VCM has 1 element(s): rest
> XTC has 1 element(s): rest
> Or. Res. Fit has 1 element(s): rest
> QMMM has 1 element(s): rest
> Checking consistency between energy and charge groups...
>
> NOTE 2 [file grompp.mdp, line unknown]:
> You are using a plain Coulomb cut-off, which might produce artifacts.
> You might want to consider using PME electrostatics.
>
>
> This run will generate roughly 1 Mb of data
> writing run input file...
>
> There were 2 notes
>
> There was 1 warning
>
> -------------------------------------------------------
> Program grompp, VERSION 4.0.4
> Source code file: gmx_fatal.c, line: 481
>
> Fatal error:
> Too many warnings (1), grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> -------------------------------------------------------
>
>
> Who can help me to solve this problem?
>
>
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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