How do I determine what those values should be? How does it affect the simulation?<div><br></div><div>thanks,</div><div><br></div><div>Ilya<br><br><div class="gmail_quote">On Fri, Apr 10, 2009 at 8:00 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
Joe Joe wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi All,<br>
<br>
I get the following error when running replica exchange. I have 32 replica's with each replica running on 4 processors (128 total). How do I decrease the domain decomposition cell size, -dss? What should I set it to?<br>
</blockquote>
<br></div>
<snip><br>
<br>
You're getting some hints from mdrun, I'd start there:<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
-------------------------------------------------------<br>
Program mdrun_mpi, VERSION 4.0.4<br>
Source code file: domdec_con.c, line: 679<br>
<br>
Fatal error:<br>
DD cell 5 0 0 could only obtain 96 of the 108 atoms that are connected via vsites from the neighboring cells. This probably means your vsite lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or use the -rcon option of mdrun.<br>
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</blockquote>
<br></div>
...So manually set -dd and/or -rcon.<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</blockquote></div><br></div>