[gmx-users] "Gromacs 4 grompp -v" err
li bai
javacfish at yahoo.com.cn
Tue Mar 10 10:32:39 CET 2009
Hello,everyone!
Sorry for the last letter!
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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