Hi Blaise,<br><br>Check for the first occurrence of the error in the log file and match the atom numbers against your .gro file to see which residue is involved from the beginning. Also, do you have non-standard residues/metal ions? Tell more about the system and what you're trying to do.
<br><br>Best,<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 10/3/07, <b class="gmail_sendername">Blaise Mathias-Costa</b> <<a href="mailto:bmathiascosta@unmc.edu">bmathiascosta@unmc.edu</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2"></font><div><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">Hello Mark and Tsjerk, Thanks a lot for your suggestions. I have gone through that web site and it doesn't say anything very specific, for example if the system is not minimized properly it should have complained at the beginning, but the problem arises after
2.6nS! </font></div><div><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">I have searched in the archive, when somebody had similar problem with PR run David suggested to look for the "center-of-mass motion removal", to give POPC+Protein, but I dont have POPC in my system. In another case advised to reduce the time step, does it mean that I should reduce the time step from
0.002 to 0.001 and do the simulations from the beginning? </font></div><div><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2"> </font></div><div><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">
Another suggestion was the computing power may not be sufficient, but I don't think this will be applicable for me, b'se I am running in 8 nodes each node is with 4 processors, and the unit cell size is ~96000 atoms in total.
</font></div><div><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2"> </font></div><div><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">What could be the most appropriate way to solve this problem? Many thanks in advance!
</font></div><div><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2"> </font></div><div><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">Kind Regards,</font></div><div><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">
Blaise</font></div><div><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2"><br></font><div><span class="q"><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">Blaise Mathias Costa, PhD
<br>Department of Pharmacology and Experimental Neuroscience<br>University of Nebraska Medical Center<br>Omaha, NE 68198-5800, USA.<br>Tel: 001 402 559 7132 <br></font><div><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">
<br></font></div></span><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2"><font color="#990099">-----<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
gmx-users-bounces@gromacs.org</a> wrote: -----<br><br></font></font><blockquote style="border-left: 2px solid rgb(0, 0, 0); padding-right: 0px; padding-left: 5px; margin-left: 5px; margin-right: 0px;"><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users@gromacs.org</a>><br>From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
Mark.Abraham@anu.edu.au</a>><br>Sent by: <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users-bounces@gromacs.org</a><br>Date: 10/02/2007 12:29PM
<br>Subject: Re: [gmx-users] mdrun error after 2.6nS</font><div><span class="e" id="q_115665412e170c71_3"><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2"><br><br><font face="Default Monospace,Courier New,Courier,monospace" size="2">
Blaise Mathias-Costa wrote:<br>> Hi all,<br>> <br>> The mdrun stopped after 2.6nS after writing this error:<br>> Step 1321571, time 2643.14 (ps) LINCS WARNING<br><br>See <a href="http://wiki.gromacs.org/index.php/Errors#LINCS_warnings" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
http://wiki.gromacs.org/index.php/Errors#LINCS_warnings</a><br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8 <br>3584 CH Utrecht<br>The Netherlands<br>
P: +31-30-2539931 <br>F: +31-30-2537623