[gmx-users] Fwd: Re: Gromacs Error
Tsjerk Wassenaar
tsjerkw at gmail.com
Tue May 19 12:42:29 CEST 2015
Please keep conversations on the mailing list. And please read the manual.
And note that the error is completely different this time.
Tsjerk
---------- Forwarded message ----------
From: "manoj damale" <manojaurangabadkar at yahoo.co.in>
Date: May 19, 2015 12:19
Subject: Re: [gmx-users] Gromacs Error
To: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
Cc:
Dear,
Sorry to distrub you,
when i have replace
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
with
rcoulomb must be <= rlist ; short-range electrostatic cutoff (in nm)
it again giving error as
WARNING 1 [file nvt.mdp, line 44]:
Unknown left-hand 'rcoulomb <' in parameter file
Program grompp, VERSION 4.5.3
Source code file: futil.c, line: 491
File input/output error:
index.ndx
With Best Regards.
Mr.Manoj Damale,
M.S. Pharma (Pharmacoinformatics) NIPER,
Kolkata, West Bengal State,
India.
On Tuesday, 19 May 2015 2:17 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
wrote:
ERROR 1 [file nvt.mdp]:
With coulombtype = PME-Switch, rcoulomb must be <= rlist
On Tue, May 19, 2015 at 10:25 AM, manoj damale <
manojaurangabadkar at yahoo.co.in> wrote:
what exactly i should modify
With Best Regards.
Mr.Manoj Damale,
M.S. Pharma (Pharmacoinformatics) NIPER,
Kolkata, West Bengal State,
India.
On Tuesday, 19 May 2015 11:32 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
wrote:
Hi Manoj,
The error is clear. Check the settings referred to in your .mdp file and
modify them accordingly.
Cheers,
Tsjerk
On May 19, 2015 07:35, "manoj damale" <manojaurangabadkar at yahoo.co.in>
wrote:
Dear All,
i'm geting below error while subjecting my system (Protein-ligand) for
equlibriation in nvt.mdp file
mgmibt at mgmibt:~/gromacs-4.5.3/recent/files$ grompp -f nvt.mdp -c em.gro -p
topol.top -n index.ndx -o nvt.tpr
:-) G R O M A C S (-:
GRowing Old MAkes el Chrono Sweat
:-) VERSION 4.5.3 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
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 nvt.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c em.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt! Index file
-p topol.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o nvt.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
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no 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'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.18#
ERROR 1 [file nvt.mdp]:
With coulombtype = PME-Switch, rcoulomb must be <= rlist
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'UNT'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...
Setting gen_seed to 3507
Velocities were taken from a Maxwell distribution at 300 K
-------------------------------------------------------
Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 1356
Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"Yeah, a Wuzz, Or a Jerk" (F. Black)
With Best Regards.
Mr.Manoj Damale,
M.S. Pharma (Pharmacoinformatics) NIPER,
Kolkata, West Bengal State,
India.
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