Hi Justin,<div><br></div><div>Thanks for helping me with this. <br><br><div class="gmail_quote">On Sat, Apr 11, 2009 at 4:46 AM, 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">
How do I determine what those values should be? How does it affect the simulation?<br>
<br>
</blockquote>
<br></div>
The header of your log file should have printed what the initial guesses were. The -dd option sets how many PP nodes there are in the domain decomposition; using 4 cores, there are probably 3 PP: 1 PME, so you probably can't tweak this option, really.</blockquote>
<div><br></div><div>I do not get it. the input to -dd is a vector. What to the elements of the vector represent?</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
<br>
The -rcon option is explained in mdrun -h or the manual. See what mdrun guessed, then increase this value.</blockquote><div><br></div><div>I tried -rcon 3.0 and got the same error. The error only occurs when I do the exchange. If I increase the replex from 500 to 1000 then I do not see the error for 1000 steps. How is the replex associated with the domain decomposition? </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
thanks,<br>
<br>
Ilya<div><div></div><div class="h5"><br>
<br>
On Fri, Apr 10, 2009 at 8:00 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Joe Joe wrote:<br>
<br>
Hi All,<br>
<br>
I get the following error when running replica exchange. I have<br>
32 replica's with each replica running on 4 processors (128<br>
total). How do I decrease the domain decomposition cell size,<br>
-dss? What should I set it to?<br>
<br>
<br>
<snip><br>
<br>
You're getting some hints from mdrun, I'd start there:<br>
<br>
<br>
-------------------------------------------------------<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<br>
connected via vsites from the neighboring cells. This probably<br>
means your vsite lengths are too long compared to the domain<br>
decomposition cell size. Decrease the number of domain<br>
decomposition grid cells or use the -rcon option of mdrun.<br>
-------------------------------------------------------<br>
<br>
<br>
...So manually set -dd and/or -rcon.<br>
<br>
-Justin<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></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><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>
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<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>
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