<br><br><div class="gmail_quote">On Sat, Apr 11, 2009 at 8:13 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;">
<br>
<br>
Joe Joe wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Hi Justin,<br>
<br>
Thanks for helping me with this. <br></div><div class="im">
On Sat, Apr 11, 2009 at 4:46 AM, 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></div><div class="im">
How do I determine what those values should be? How does it<br>
affect the simulation?<br>
<br>
<br>
The header of your log file should have printed what the initial<br>
guesses were. The -dd option sets how many PP nodes there are in the<br>
domain decomposition; using 4 cores, there are probably 3 PP: 1 PME,<br>
so you probably can't tweak this option, really.<br>
<br>
<br>
I do not get it. the input to -dd is a vector. What to the elements of the vector represent?<br>
</div></blockquote>
<br>
The number of DD grid cells per axis. For example, 3 1 1 means 2 divisions along the x axis to give 3 DD cells, 1 cell in each the y- and z-axis for a total of 3 cells. -dd 3 2 1 gives 3 x-cells, 2 y-cells, and 1 z-cell for a total of 6 DD cells.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
<br>
The -rcon option is explained in mdrun -h or the manual. See what<br>
mdrun guessed, then increase this value.<br>
<br>
<br>
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?<br>
</blockquote>
<br></div>
I don't know the specifics here. There may be some incompatibility between DD and virtual sites; I know there were some bugs in previous versions. What kind of virtual sites are you using? Does the run work successfully with -dd turned off (i.e., mdrun -pd)?</blockquote>
<div><br></div><div>I am using pdb2gmx -vsite h so I can run 4fs time steps, so virtual hydrogens. I will try with -pd and see what happens. </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
<br>
-Justin<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
<br>
<br>
<br>
-Justin<br>
<br>
thanks,<br>
<br>
Ilya<br>
<br>
<br>
On Fri, Apr 10, 2009 at 8:00 PM, Justin A. Lemkul<br>
<<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>><br></div><div><div></div><div class="h5">
<mailto:<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.<br>
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<br>
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>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<div class="im">
<br>
231-9080<br>
<br>
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-- ========================================<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> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
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-- <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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