<br> Thank You for Quick reply Justin...<br><br><div class="gmail_quote">On Sat, Jun 2, 2012 at 8:58 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"><br>
You'll get a mismatch in your files (checkpoint, trajectory, energy) in terms of frame interval. You should not try to append to these files or extend the run. Just run a new simulation from 20 -> 30 ns. The grompp command was correct, assuming you set "tinit = 20000" in the .mdp file and setting nsteps appropriately to give another 10 ns. Then run it as a new simulation. It will still be an extension of the first simulation (since the .cpt preserves the previous state), but without the mdrun -cpi -append mechanism, which in this case you don't want (or possibly can't use)</blockquote>
<div><br>I will follow your advice..<br><br><br><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:0 0 0 .8ex;border-left:1px #ccc solid;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>
<br>
Use gmxcheck to understand the contents of each. The timestamp will also<br>
tell you a difference, as will reading mdrun -h for an explanation of what<br>
the -cpt option is doing<br>
<br>
<br>
As per the link..<a href="http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File" target="_blank">http://www.gromacs.org/<u></u>Documentation/File_Formats/<u></u>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<br>
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<br>
them ??<br>
<br>
Crash the run is very often with my system, that why I am worried..<br>
<br>
</blockquote>
<br></div>
If you're getting frequent crashes, you should investigate why this is happening rather than just plowing ahead. Are there error messages in the .log or stdout/stderr output? Are your energetic terms sensible? If the system is crashing due to physical instability, you're wasting your time producing junk. If the crashes are occurring due to hardware or filesystem instability, that's something to take up with your sysadmin.<div class="HOEnZb">
<div class="h5"><br>
<br>
-Justin<br></div></div></blockquote><div>Thank you For Advice...<br></div></div>