Uday,
You are reproducing the output of md.csh. I would also like to see the
contents of md.csh to know the gromacs commands therein. This would help to see
where the error is coming. Please paste the file md.csh.
sharada
-- Original Message --
From: udaya kiran <[email protected]>
To: Sarath Chandra
<[email protected]>
Cc: Discussion list for GROMACS users
<[email protected]>
Date: Tue, 14 Dec 2010 11:13:05 +0100
Subject: Re: [gmx-users] ERROR: Source code
file: statutil.c, line: 727
Hello,
Here I am sending the complete output after the
md.csh command with the errors in bold.
COMMAND: csh md.csh
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.5 (-:
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>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 (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-f md-md.mdp Input, Opt! grompp input file with
MD parameters
-po inmd.mdp Output grompp input file with MD
parameters
-c results/eq1bar300K.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_sol.ndx Input, Opt! Index file
-p topol_sol_hbond_131210.top Input Topology
file
-pp processed.top Output, Opt. Topology file
-o inmd.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
ERROR
-------------------------------------------------------
Program grompp, VERSION 4.0.5
Source code file: statutil.c, line: 727
Invalid command line argument:
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
[1] 16658
: Command not found.
:-) G R O M A C S (-:
Great Red Oystrich Makes All Chemists Sane
:-) VERSION 4.0.5 (-:
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>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.
:-) mdrun (double precision) (-:
achje05
(/loch/akbl1/marelli/PROJECTS/16L4_16_aAALAA/16L4_GROMACS_RUN_HB3_131210)>
Option Filename Type Description
------------------------------------------------------------
-s inmd.tpr Input Run input file: tpr tpb tpa
-o MDResults/md.trr Output Full precision
trajectory: trr trj cpt
-x MDResults/md.xtc Output, Opt. Compressed
trajectory (portable xdr
format)
-cpi MDResults/md.cpt Input, Opt. Checkpoint
file
-cpo MDResults/md.cpt Output, Opt. Checkpoint
file
-c MDResults/md.gro Output Structure file: gro
g96 pdb
-e MDResults/md.edr Output Energy file: edr ene
-g MDResults/md.log Output Log file
-dgdl MDResults/md.xvg Output, Opt. xvgr/xmgr
file
-field MDResults/md.xvg Output, Opt. xvgr/xmgr
file
-table MDResults/md.xvg Input, Opt. xvgr/xmgr
file
-tablep MDResults/md.xvg Input, Opt. xvgr/xmgr
file
-tableb MDResults/md.xvg Input, Opt. xvgr/xmgr
file
-rerun MDResults/md.xtc Input, Opt. Trajectory:
xtc trr trj gro g96 pdb cpt
-tpi MDResults/md.xvg Output, Opt. xvgr/xmgr
file
-tpid MDResults/md.xvg Output, Opt. xvgr/xmgr
file
-ei MDResults/md.edi Input, Opt. ED sampling
input
-eo MDResults/md.edo Output, Opt. ED sampling
output
-j MDResults/md.gct Input, Opt. General
coupling stuff
-jo MDResults/md.gct Output, Opt. General
coupling stuff
-ffout MDResults/md.xvg Output, Opt. xvgr/xmgr
file
-devout MDResults/md.xvg Output, Opt. xvgr/xmgr
file
-runav MDResults/md.xvg Output, Opt. xvgr/xmgr
file
-px MDResults/md.xvg Output, Opt. xvgr/xmgr file
-pf MDResults/md.xvg Output, Opt. xvgr/xmgr file
-mtx MDResults/md.mtx Output, Opt. Hessian
matrix
-dn MDResults/md.ndx Output, Opt. Index file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-deffnm string MDResults/md Set the default
filename for all file
options
-[no]xvgr bool yes Add specific codes (legends
etc.) in the output
xvg files for the xmgrace program
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0
is optimize
-npme int -1 Number of separate nodes to be
used for PME, -1
is guess
-ddorder enum interleave DD node order:
interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded
interactions with DD
-rdd real 0 The maximum distance for bonded
interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm),
0 is estimate
-dlb enum auto Dynamic load balancing (with
DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of
the DD cell size
-[no]sum bool yes Sum the energies at every step
-[no]v bool no Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl
terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than
this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations
that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]append bool no Append to previous output
files when continuing
from checkpoint
-[no]addpart bool yes Add the simulation part
number to all output
files when continuing from checkpoint
-maxh real -1 Terminate after 0.99 times this
time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange every #
steps
-reseed int -1 Seed for replica exchange, -1 is
generate a seed
-[no]glas bool no Do glass simulation with
special long range
corrections
-[no]ionize bool no Do a simulation including
the effect of an X-Ray
bombardment on your system
Back Off! I just backed up MDResults/md.log to
MDResults/#md.log.3#
ERROR
-------------------------------------------------------
Program mdrun, VERSION 4.0.5
Source code file: gmxfio.c, line: 736
Can not open file:
inmd.tpr
-------------------------------------------------------
"And You Will Know That My Name is the Lord
When I Lay My Vengeance Upon Thee." (Pulp Fiction)
yours sincerely,
uday.
On Tue, Dec 14, 2010 at 11:05 AM,
Sarath Chandra <<[email protected]>[email protected]>
wrote:
On Tue, Dec 14,
2010 at 10:07 AM, udaya kiran <<[email protected]>[email protected]>
wrote:
Hello
madam,
The
command id
csh
md.csh
Please paste
your md.csh file and the error you get in detail.
As I
see, there is no error in the command. All other commands are properly working
(like eq.csh, em.csh etc ). The problem is only with md.csh.
yours
sincerely,
uday.
--
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Best Wishes,
Sarath
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