<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY>Uday,<br >
<br >
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.<br >
<br >
sharada<br >
<br >
<TABLE STYLE="padding-left: 5px; border-bottom-color: blue; border-left: blue 1px solid; border-top-color: blue; border-right-color: blue">
<tbody>
<TR>
<TD>
<br >
<font face="Arial" size="2"><b><i>-- Original Message --</i></b><br >
From: udaya kiran <kiran.udaya@gmail.com><br >
To: Sarath Chandra <sarathchandradantu@gmail.com><br >
Cc: Discussion list for GROMACS users <gmx-users@gromacs.org><br >
Date: Tue, 14 Dec 2010 11:13:05 +0100<br >
Subject: Re: [gmx-users] ERROR: Source code file: statutil.c, line: 727<br >
<br >
Hello,<br >
<br >
Here I am sending the complete output after the md.csh command with the errors in bold.<br >
<br >
<br >
COMMAND: csh md.csh<br >
<br >
<br >
:-) G R O M A C S (-:<br >
<br >
Groningen Machine for Chemical Simulation<br >
<br >
:-) VERSION 4.0.5 (-:<br >
<br >
<br >
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br >
Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br >
Copyright (c) 2001-2008, The GROMACS development team,<br >
check out <A TARGET="_blank" HREF="http://www.gromacs.org">http://www.gromacs.org</A> for more information.<br >
<br >
This program is free software; you can redistribute it and/or<br >
modify it under the terms of the GNU General Public License<br >
as published by the Free Software Foundation; either version 2<br >
of the License, or (at your option) any later version.<br >
<br >
:-) grompp (double precision) (-:<br >
<br >
Option Filename Type Description<br >
------------------------------------------------------------<br >
-f md-md.mdp Input, Opt! grompp input file with MD parameters<br >
-po inmd.mdp Output grompp input file with MD parameters<br >
-c results/eq1bar300K.gro Input Structure file: gro g96 pdb tpr tpb<br >
tpa<br >
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br >
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br >
-n Index_sol.ndx Input, Opt! Index file<br >
-p topol_sol_hbond_131210.top Input Topology file<br >
-pp processed.top Output, Opt. Topology file<br >
-o inmd.tpr Output Run input file: tpr tpb tpa<br >
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt<br >
-e ener.edr Input, Opt. Energy file: edr ene<br >
<br >
Option Type Value Description<br >
------------------------------------------------------<br >
-[no]h bool no Print help info and quit<br >
-nice int 0 Set the nicelevel<br >
-[no]v bool yes Be loud and noisy<br >
-time real -1 Take frame at or first after this time.<br >
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual<br >
sites<br >
-maxwarn int 0 Number of allowed warnings during input processing<br >
-[no]zero bool no Set parameters for bonded interactions without<br >
defaults to zero instead of generating an error<br >
-[no]renum bool yes Renumber atomtypes and minimize number of<br >
atomtypes<br >
<br >
<b>ERROR<br >
-------------------------------------------------------<br >
Program grompp, VERSION 4.0.5<br >
Source code file: statutil.c, line: 727<br >
<br >
Invalid command line argument:<br >
<br >
-------------------------------------------------------</b><br >
<br >
Thanx for Using GROMACS - Have a Nice Day<br >
<br >
[1] 16658<br >
: Command not found.<br >
:-) G R O M A C S (-:<br >
<br >
Great Red Oystrich Makes All Chemists Sane<br >
<br >
:-) VERSION 4.0.5 (-:<br >
<br >
<br >
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br >
Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br >
Copyright (c) 2001-2008, The GROMACS development team,<br >
check out <A TARGET="_blank" HREF="http://www.gromacs.org">http://www.gromacs.org</A> for more information.<br >
<br >
This program is free software; you can redistribute it and/or<br >
modify it under the terms of the GNU General Public License<br >
as published by the Free Software Foundation; either version 2<br >
of the License, or (at your option) any later version.<br >
<br >
:-) mdrun (double precision) (-:<br >
<br >
achje05 (/loch/akbl1/marelli/PROJECTS/16L4_16_aAALAA/16L4_GROMACS_RUN_HB3_131210)> Option Filename Type Description<br >
------------------------------------------------------------<br >
-s inmd.tpr Input Run input file: tpr tpb tpa<br >
-o MDResults/md.trr Output Full precision trajectory: trr trj cpt<br >
-x MDResults/md.xtc Output, Opt. Compressed trajectory (portable xdr<br >
format)<br >
-cpi MDResults/md.cpt Input, Opt. Checkpoint file<br >
-cpo MDResults/md.cpt Output, Opt. Checkpoint file<br >
-c MDResults/md.gro Output Structure file: gro g96 pdb<br >
-e MDResults/md.edr Output Energy file: edr ene<br >
-g MDResults/md.log Output Log file<br >
-dgdl MDResults/md.xvg Output, Opt. xvgr/xmgr file<br >
-field MDResults/md.xvg Output, Opt. xvgr/xmgr file<br >
-table MDResults/md.xvg Input, Opt. xvgr/xmgr file<br >
-tablep MDResults/md.xvg Input, Opt. xvgr/xmgr file<br >
-tableb MDResults/md.xvg Input, Opt. xvgr/xmgr file<br >
-rerun MDResults/md.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt<br >
-tpi MDResults/md.xvg Output, Opt. xvgr/xmgr file<br >
-tpid MDResults/md.xvg Output, Opt. xvgr/xmgr file<br >
-ei MDResults/md.edi Input, Opt. ED sampling input<br >
-eo MDResults/md.edo Output, Opt. ED sampling output<br >
-j MDResults/md.gct Input, Opt. General coupling stuff<br >
-jo MDResults/md.gct Output, Opt. General coupling stuff<br >
-ffout MDResults/md.xvg Output, Opt. xvgr/xmgr file<br >
-devout MDResults/md.xvg Output, Opt. xvgr/xmgr file<br >
-runav MDResults/md.xvg Output, Opt. xvgr/xmgr file<br >
-px MDResults/md.xvg Output, Opt. xvgr/xmgr file<br >
-pf MDResults/md.xvg Output, Opt. xvgr/xmgr file<br >
-mtx MDResults/md.mtx Output, Opt. Hessian matrix<br >
-dn MDResults/md.ndx Output, Opt. Index file<br >
<br >
Option Type Value Description<br >
------------------------------------------------------<br >
-[no]h bool no Print help info and quit<br >
-nice int 19 Set the nicelevel<br >
-deffnm string MDResults/md Set the default filename for all file<br >
options<br >
-[no]xvgr bool yes Add specific codes (legends etc.) in the output<br >
xvg files for the xmgrace program<br >
-[no]pd bool no Use particle decompostion<br >
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize<br >
-npme int -1 Number of separate nodes to be used for PME, -1<br >
is guess<br >
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian<br >
-[no]ddcheck bool yes Check for all bonded interactions with DD<br >
-rdd real 0 The maximum distance for bonded interactions with<br >
DD (nm), 0 is determine from initial coordinates<br >
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate<br >
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes<br >
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size<br >
-[no]sum bool yes Sum the energies at every step<br >
-[no]v bool no Be loud and noisy<br >
-[no]compact bool yes Write a compact log file<br >
-[no]seppot bool no Write separate V and dVdl terms for each<br >
interaction type and node to the log file(s)<br >
-pforce real -1 Print all forces larger than this (kJ/mol nm)<br >
-[no]reprod bool no Try to avoid optimizations that affect binary<br >
reproducibility<br >
-cpt real 15 Checkpoint interval (minutes)<br >
-[no]append bool no Append to previous output files when continuing<br >
from checkpoint<br >
-[no]addpart bool yes Add the simulation part number to all output<br >
files when continuing from checkpoint<br >
-maxh real -1 Terminate after 0.99 times this time (hours)<br >
-multi int 0 Do multiple simulations in parallel<br >
-replex int 0 Attempt replica exchange every # steps<br >
-reseed int -1 Seed for replica exchange, -1 is generate a seed<br >
-[no]glas bool no Do glass simulation with special long range<br >
corrections<br >
-[no]ionize bool no Do a simulation including the effect of an X-Ray<br >
bombardment on your system<br >
<br >
<br >
Back Off! I just backed up MDResults/md.log to MDResults/#md.log.3#<br >
<br >
<b>ERROR<br >
-------------------------------------------------------<br >
Program mdrun, VERSION 4.0.5<br >
Source code file: gmxfio.c, line: 736<br >
<br >
Can not open file:<br >
inmd.tpr<br >
-------------------------------------------------------</b><br >
<br >
"And You Will Know That My Name is the Lord When I Lay My Vengeance Upon Thee." (Pulp Fiction)<br >
<br >
<br >
<br >
<br >
yours sincerely,<br >
uday.</font><br >
<br >
<br >
<DIV CLASS="gmail_quote">
<font face="Arial" size="2">On Tue, Dec 14, 2010 at 11:05 AM, Sarath Chandra <SPAN DIR="ltr"><<A TARGET="_blank" HREF="mailto:sarathchandradantu@gmail.com">sarathchandradantu@gmail.com</A>></SPAN> wrote:</font><br >
<blockquote class="gmail_quote" style="padding-left: 1ex; margin: 0pt 0pt 0pt 0.8ex; border-left: rgb(204,204,204) 1px solid">
<br >
<br >
<DIV CLASS="gmail_quote">
<DIV CLASS="im">
<font face="Arial" size="2">On Tue, Dec 14, 2010 at 10:07 AM, udaya kiran <SPAN DIR="ltr"><<A TARGET="_blank" HREF="mailto:kiran.udaya@gmail.com">kiran.udaya@gmail.com</A>></SPAN> wrote:</font><br >
<blockquote class="gmail_quote" style="padding-left: 1ex; margin: 0pt 0pt 0pt 0.8ex; border-left: rgb(204,204,204) 1px solid">
<font face="Arial" size="2">Hello madam,<br >
<br >
The command id<br >
<br >
<i>csh</i> <i>md.csh</i></font><br >
</blockquote>
</DIV>
<DIV>
<br >
<font face="Arial" size="2">Please paste your md.csh file and the error you get in detail.</font></DIV>
<blockquote class="gmail_quote" style="padding-left: 1ex; margin: 0pt 0pt 0pt 0.8ex; border-left: rgb(204,204,204) 1px solid">
<DIV CLASS="im">
<font face="Arial" size="2">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.<br >
<br >
yours sincerely,<br >
uday.</font><br >
</DIV>
<font face="Arial" size="2">--<br >
gmx-users mailing list <A TARGET="_blank" HREF="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><br >
<A TARGET="_blank" HREF="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</A><br >
Please search the archive at <A TARGET="_blank" HREF="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</A> before posting!<br >
Please don't post (un)subscribe requests to the list. Use the<br >
www interface or send it to <A TARGET="_blank" HREF="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<br >
Can't post? Read <A TARGET="_blank" HREF="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</A></font></blockquote>
</DIV>
<br >
<br >
<font face="Arial" size="2">Best Wishes,<br >
<br >
<br >
<font color="#888888">Sarath</font></font></blockquote>
</DIV>
<br >
<font face="Arial" size="2">--<br >
gmx-users mailing list gmx-users@gromacs.org<br >
http://lists.gromacs.org/mailman/listinfo/gmx-users<br >
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br >
Please don't post (un)subscribe requests to the list. Use the<br >
www interface or send it to gmx-users-request@gromacs.org.<br >
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists</font></TD>
</TR>
</tbody>
</TABLE>
<BR>
"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."
<BR></BODY></HTML>