nitu sharma wrote:
Dear all,
I have successfully installed the gromacs 4.0.3
it is working but the problem is when I want to run the gromacs demo
during processing when I put the command "grompp -v" the output like
this ,:-) G R O M A C S (-:
Gromacs Runs On Most of All Computer Systems
:-) VERSION 4.0.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, 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'
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 /usr/local/gromacs/share/gromacs/top/ffgmx.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxnb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxbon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Opening library file /usr/local/gromacs/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 /usr/local/gromacs/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, this will often 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 4.0.3
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.
-------------------------------------------------------
"How Do You Like Your Vacation So Far ?" (Speed 2 - Cruise Control) why
the grompp -v terminated even i am going step by step as in mannual.
could you please anybody tell me about that.
Thank you very much in advance.
The existence of this list doesn't mean you don't have to do your own
detective work! Nobody's paying any of us to help anybody, and we'll be
much more inclined to give our valuable time to you if you've
demonstrated a genuine attempt to solve your own problem.
This error message is explicit. There's a fatal error because there's
too many warnings. There's one warning given. Read it and draw your own
conclusions :-)
Whatever demonstration you're doing was also probably written for a
GROMACS version below 4, so you should expect some differences.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
