Dear Justin,<br><br>Thanks for the fast response. The exact command I used is :<br><br>mdrun -v -s eq2.tpr -deffnm eq2 -g eq2.log -nice 19 >& eq2.out &<br><br>Regards,<br><br>Ozlem<br><br><div class="gmail_quote">
On Wed, May 4, 2011 at 3:23 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>
Ozlem Ulucan wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Dear Gromacs Users,<br>
<br>
I have been trying to simulate a protein in implicit solvent. When I used a single processor by setting -nt to 1 , I did not encounter any problem. But when I tried to run the simulations using more than 1 processor I get the following error.<br>
<br>
Fatal error:<br>
Constraint dependencies further away than next-neighbor<br>
in particle decomposition. Constraint between atoms 2177--2179 evaluated<br>
on node 3 and 3, but atom 2177 has connections within 4 bonds (lincs_order)<br>
of node 1, and atom 2179 has connections within 4 bonds of node 3.<br>
Reduce the # nodes, lincs_order, or<br>
try domain decomposition.<br>
<br>
I set the lincs_order parameter in .mdp file to different values. But it did not help. I have some questions regarding the information above.<br>
<br>
1) Is it possible to run implicit solvent simulations in parallel?<br>
<br>
</blockquote>
<br></div>
Yes.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
2) As far as I know gromacs uses domain decomposition as default. Why does in my simulations gromacs use the particle decomposition which I do not ask for.<br>
<br>
</blockquote>
<br></div>
Without seeing the exact commands you gave, there is no plausible explanation. DD is used by default.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Any suggestions are appreciated very much.<br>
I am ussing gromacs-4.5.4 with charmm force field and the OBC implicit solvent model. If you need further informations, probably a run input file, let me know.<br>
<br>
Regards,<br>
<br>
Ozlem Ulucan<br>
<br>
</blockquote>
<br></div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<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="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><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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