[gmx-users] ERROR: Source code file: statutil.c, line: 727
sharada
sharada at ccmb.res.in
Wed Dec 15 07:30:52 CET 2010
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 <kiran.udaya at gmail.com>
To: Sarath Chandra <sarathchandradantu at gmail.com>
Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
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 <<sarathchandradantu at gmail.com>sarathchandradantu at gmail.com> wrote:
On Tue, Dec 14, 2010 at 10:07 AM, udaya kiran <<kiran.udaya at gmail.com>kiran.udaya at gmail.com> 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.
--
gmx-users mailing list <gmx-users at gromacs.org>gmx-users at gromacs.org
<http://lists.gromacs.org/mailman/listinfo/gmx-users>http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at <http://www.gromacs.org/Support/Mailing_Lists/Search>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <gmx-users-request at gromacs.org>gmx-users-request at gromacs.org.
Can't post? Read <http://www.gromacs.org/Support/Mailing_Lists>http://www.gromacs.org/Support/Mailing_Lists
Best Wishes,
Sarath
--
gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
"The person addressed in the email is the sole authorized recipient.
Should you receive it in error, immediately notify the sender of the
error and delete the e-mail. Any unauthorized dissemination or copying
of this e-mail (or any attachment to this e-mail) or the wrongful
disclosure of the information herein contained is prohibited.
Also note that this form of communication is not secure, it can be
intercepted, and may not necessarily be free of errors and viruses
in spite of reasonable efforts to secure this medium."
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101215/65c75aeb/attachment.html>
More information about the gromacs.org_gmx-users
mailing list