Thank you Justin for quick reply ....<br><br><div class="gmail_quote">On Sat, Jun 2, 2012 at 8:12 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">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>
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To perform these task I am using following command<br>
1. grompp -f <New mdp file just change in saving output> -t <.cpt> -c <.gro<br>
file(gro file from position restrained run )> -o new.tpr<br>
<br>
<br>
2. tpbconv -s new.tpr -0 extend.tpr -extend 30000<br>
<br>
3. mdrun -v -deffnm extend -cpi <.cpt> -append<br>
<br>
Is these approach is correct??<br>
<br>
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No. The new.tpr file contains instructions to run from 20 -> 30 ns. There is no need to then invoke tpbconv. You would also need a new invocation of mdrun, since the output frequencies won't match. You don't want to append those files with mdrun (nor will the checkpoint file likely let you)</blockquote>
<div><br>Extremely Sorry for my carelessness , New mdp files means the same as previous, with same number of steps, but just change in output frequency <br><br>So as per your recommendation and experience Is any alternative to do these from 20 ns??? <br>
</div><div><br> </div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="im"><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Second query;<br>
<br>
To rerun the crash run, users give .cpt file as input to -mdrun,<br>
My query is, There are two cpt file a) pre.cpt b) .cpt ,<br>
So which one has to given as input???<br>
<br>
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Use gmxcheck to understand the contents of each. The timestamp will also tell you a difference, as will reading mdrun -h for an explanation of what the -cpt option is doing</blockquote><div><br>As per the link..<a href="http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File">http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File</a><br>
I interpreted following things..<br><br>1. I have to use the state.cpt , but in the case problem to these I have to use prev.cpt, I can check there <br> content by gmxcheck..<br><br> But my Query is What are may be the potential problems ?? and how to find them ??<br>
<br>Crash the run is very often with my system, that why I am worried..<br> <br></div></div>