Thanks Justin, you are very helpful as always :-)<br><br><div class="gmail_quote">On Thu, Sep 24, 2009 at 6:41 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>
Jack Shultz wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
If I run a simulation using mdrun and then run mdrun again, does it add another interval of simulation or does it just re-run the last simulation. I'll elaborate so it makes a little more sense, our project has this progress bar that tells users the progress of the simulation. If I run mdrun for 100ps they will think it is stuck in an endless loop. If we run increments of mdrun, we can update the bar at each increment. Can we go straight to mdrun or do we have to prep the next increment with grompp?<br>
<br>
</blockquote>
<br></div>
You have to make use of checkpointing. This page might be useful:<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Extending_Simulations" target="_blank">http://www.gromacs.org/Documentation/How-tos/Extending_Simulations</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
-- <br>
Jack<br>
<br>
<a href="http://drugdiscoveryathome.com" target="_blank">http://drugdiscoveryathome.com</a><br>
<a href="http://hydrogenathome.org" target="_blank">http://hydrogenathome.org</a><br>
<br>
<br></div>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<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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</blockquote></div><br><br clear="all"><br>-- <br>Jack<br><br><a href="http://drugdiscoveryathome.com">http://drugdiscoveryathome.com</a><br><a href="http://hydrogenathome.org">http://hydrogenathome.org</a><br>