<div>Thanks Justin for being so patient. I have understood almost everything and I hope this is the last question on this thread.</div>
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<div>See inline ...<br></div>
<div class="gmail_quote">On Wed, Feb 2, 2011 at 5:53 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="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br><br>Sai Pooja wrote:
<div><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"> On Wed, Feb 2, 2011 at 3:15 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
<br> On 3/02/2011 6:15 AM, Sai Pooja wrote:<br><br> The problem is solved with grompp i.e. I use the -t .cpt option.<br> However, now appending does not work. I remember Mark said in a<br> previous mail that a certain environment variable can allow<br>
appending to happen even in such cases. I would liek to try that<br> out.<br><br> No, I said that an environment variable can override the mechanism<br> that blocks ensemble changes in mdrun.<br><br> So how can I use this environment variable.. I might be asking an absurd question since I don't really understand what an environment variable is. But I would definitely liek to experiment with it, since I am in the process of trying out these different options and figuring out which would be the best.<br>
<br></blockquote><br></div><a href="http://en.wikipedia.org/wiki/Environment_variable" target="_blank">http://en.wikipedia.org/wiki/Environment_variable</a><br><br>I think the pertinent one in this case is GMX_ALLOW_CPT_MISMATCH. There is a reason these aren't well-documented; they probably shouldn't be used in most cases. You should have seen a very specific error message in your .log file or screen output indicating that this situation was relevant (src/gmxlib/checkpoint.c, around line 1606).
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<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">I also need to understand something. What exactly does the tpbconv do when only -s and -nsteps or -extend options are supplied - it seems that it takes all the information(mass, topology, restraints) from the previous tpr file and just changes the init_step parameter and the number of steps till which the simulation should run.<br>
<br></blockquote><br></div>All it does is modify the number of steps specified in the input file; init_step should be untouched. The step from which the simulation is continued is in the .cpt file.
<div><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Now if that is the case, I am still unable to understand that if the cpt file is NOT provided to mdrun (or a mismatched one is provided), how does mdrun obtain the coordinates, velocities, box-dimensions of the last frame. If it doesn't use the ones of the last frame, what does it really use?<br>
<br></blockquote><br></div>These are two cases. If (1) an invalid .cpt file is provided, the simulation should stop with a fatal error (in checkpoint.c, described above); if (2) a checkpoint is not provided at all, then a completely new simulation is started, and the "last frame" is non-existent. The simulation begins at time zero.
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<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">If it gets them from the new_tpr file, and the new_tpr file gets it from previous_tpr file via tpbconv, then how does that ensure continuation from the last frame, because the previous_tpr file might have been compiled even before the simulation started. And as far as I know, it is purely an input file to mdrun and has no information on the last coordinates/velocities of the mdrun.<br>
</blockquote><br></div>If you provide a .tpr file to mdrun and the checkpoint file is invalid, the simulation should have stopped, per the fatal error given in checkpoint.c (described above). The contents of your .log file should make clear exactly what mdrun is doing and where it's starting.<br>
</blockquote>
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<div>In my case, I use tpbconv with just nsteps and old_tpr and supply the exchanged .cpt file. Mdrun does not crash, but none of the files get appended. All files start from the first continuation step. The logfile has no error. Same is the case with the #rexlog0.log# file which is the logfile which gets overwritten. I don't know what conclusion to draw - would it make sense to compare the last frame in the .cpt file and the first frame in the new xtc file? Should they match if the cpt file has infact been used by mdrun?</div>
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<div>Pooja</div>
<div> </div>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>In the case you describe, "new.tpr" and "previous.tpr" differ only in the number of steps, therefore the state contained therein corresponds to the beginning of the simulation, i.e. time zero.<br>
<font color="#888888"><br>-Justin</font>
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<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"> You may have answered this before but I have tried and failed in understanding. I would request you to help me in understanding the above. I would really appreciate it.<br>
Regards<br>Pooja<br><br></blockquote><br></div>
<div>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<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><br>========================================<br>-- <br></div>
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