<font color="#000099"><font face="verdana,sans-serif">After running for more than 12 hours, the REMD simulation is completed and what I get is 50 log, 50 trr, 50 cpt and 50 tpr files.</font></font><div><font color="#000099"><font face="verdana,sans-serif">Not sure if the result is reasonable.</font></font></div>
<div><font color="#000099"><font face="verdana,sans-serif"><br></font></font></div><div><font color="#000099"><font face="verdana,sans-serif">I tried to analyze the result, and after applying <a href="http://demux.pl">demux.pl</a>, two files replica_index.xvg replica_temp.xvg are obtained.</font></font></div>
<div><font color="#000099"><font face="verdana,sans-serif"><br></font></font></div><div><font color="#000099"><font face="verdana,sans-serif">My question is how to obtain the structure information? (I will need pdb file).<br>
</font></font><br><div class="gmail_quote">On Thu, Sep 29, 2011 at 6:23 AM, Manuel Prinz <span dir="ltr"><<a href="mailto:manuel@pinguinkiste.de">manuel@pinguinkiste.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Am Do, 29.09.2011, 01:38 schrieb Mark Abraham:<br>
<div class="im">> If the MPI configuration allows physical processors to be<br>
> over-allocated, then GROMACS is none the wiser.<br>
<br>
</div>Over-allocation is the default in Open MPI[1]. So it's technically<br>
possible to run 50 MPI processes on 2 cores. Whether or not this is a good<br>
idea is left on as an exercise to the reader. ;)<br>
<br>
Best regards,<br>
Manuel<br>
<br>
[1] When not run from a resource manager that takes care of setting the<br>
"right" configuration options.<br>
<div><div></div><div class="h5"><br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Best,<br>Liang Liu<br>
</div>