My time step is 1 fs. And the md0.log doesn't have anything about replica exchange which I suppose means that its not doing replica exchange.<br><br>In my other simulation, (100 ns duration and 1 fs time step), replica exchange is initialized but the exchange frequency is 10^9 (so I am not actually doing a replica exchange, but I have the conditions for that.) <br>
Is it possible that the parallel replicas can go to different time steps during the simulation if the simulation is a replica exchange one but no exchanges are attempted during the duration of the simulation.<br><br>Thanks for the help. All suggestions were really helpful.<br>
<br>Thanks,<br>Nimesh<br><br><br><div class="gmail_quote">On Tue, Aug 3, 2010 at 10:23 AM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">On 2010-08-03 17.17, Nimesh Jain wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
And the simulation is for 100ns.<br>
</blockquote></div>
So you are trying exchanges ecery 2 ns (assuming 2 fs timestep). That is rather long. If you check the file md0.log you can see whether the repl. exch. code is initialized at all. If that is the case then I guess you are seeing output file buffering (check dates on your files: the shorter ones should be older). If not something else is wrong.<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
<br>
On Tue, Aug 3, 2010 at 10:17 AM, Nimesh Jain<br>
<<a href="mailto:nimeshjain2010@u.northwestern.edu" target="_blank">nimeshjain2010@u.northwestern.edu</a><br></div><div class="im">
<mailto:<a href="mailto:nimeshjain2010@u.northwestern.edu" target="_blank">nimeshjain2010@u.northwestern.edu</a>>> wrote:<br>
<br>
mdrun command I am using: (I have a shell script that adds jobs on<br>
the server) Following are the contents of that:<br>
<br>
#!/bin/bash<br>
#<br>
#$ -cwd<br>
#$ -j y<br>
#$ -S /bin/bash<br>
#$ -pe mpi 8<br>
<br>
echo $TMP > info1<br>
<br>
unset SGE_ROOT<br>
<br>
cp $TMP/machines .<br>
<br>
MPI_DIR=/opt/openmpi/<br>
<br>
$MPI_DIR/bin/mpirun -np $NSLOTS -machinefile $PWD/machines \<br>
/share/apps/gromacs-4.0.5/bin/mdrun_mpi \<br>
-s topol_.tpr -multi 8 -pd replex 1000000<br>
<br>
<br>
Thanks,<br>
Nimesh<br>
<br>
<br>
<br>
On Tue, Aug 3, 2010 at 10:11 AM, David van der Spoel<br></div><div class="im">
<<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>> wrote:<br>
<br>
On 2010-08-03 17.08, Nimesh Jain wrote:<br>
<br>
Hi,<br>
<br>
I am doing a replica exchange simulation with 8 replicas. I<br>
was looking<br>
at my data and I observed that a couple of replicas are<br>
around 10 and 20<br>
ns ahead of everything else. Is it normal or is this wrong ?<br>
Please let me know.<br>
<br>
Thanks,<br>
Nimesh<br>
<br>
What frequency of exchange do you use?<br>
Please give mdrun command line<br>
<br>
--<br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br></div>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>><div class="im"><br>
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<br>
<br>
<br>
<br>
<br>
--<br>
Nimesh Jain<br>
Graduate Student<br>
Biomedical Engineering<br>
Northwestern University<br>
<br>
</div></blockquote><div><div></div><div class="h5">
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
-- <br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Nimesh Jain<br>Graduate Student<br>Biomedical Engineering<br>Northwestern University<br>