<p>Hey :)</p>
<p>I see that I never stated to run the production run... But at that point in the tutorial there have been several equilibration runs already, so it should be trivial to figure it out. Yet I'll add a small paragraph at the end of the production run section.<br>
Thanks for the interest in the tutorial. I hope it's good for you.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Apr 15, 2011 10:04 PM, "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br><br><br>
<br>
Monisha Hajra wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Justin,<br>
<br>
I am trying to follow the protocol only.<br>
More than the Gromacs own website, I find <a href="http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html#production" target="_blank">http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html#production</a> link is more useful.<br>
<br>
</blockquote>
<br>
Clearly. This is one of many tutorials linked from the site I posted before.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
However, I am stuck at one step which is mentioned :<br>
<a href="http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis.html" target="_blank">http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis.html</a><br>
<br>
I am not able to understand how to create traj.trr, traj.xtc and ener.edr file. Remaining all is self explained in the previous link.<br>
<br>
</blockquote>
<br>
These files are output by mdrun, i.e. actually running a simulation.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Really appreciate any help.<br>
<br>
Regards<br>
Monisha<p><font color="#500050">
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Justin A. Lemkul
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