Hi,<br><br>
<div class="gmail_quote">On Wed, Jul 22, 2009 at 1:13 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">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">
<div class="im"><br><br>Jamie Seyed wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Thank you Justin,<br> But how I can prevent from that (filesystem blip) to happen. Also May I <br></blockquote>
<br></div>I know nothing about your filesystem, but sometimes these things happen randomly. Try re-running with nstxout at some value other than zero and see if you get a non-empty .trr file. </blockquote>
<div> </div>
<div>Yes, It is ok now. I re-run it with nonzero nstxout ! Thanks for all comments.</div>
<div> </div>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im">
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">change Pcoupl= Parrinello-rahman instead of berendsen (has it any effect?? since I have changed Tcoupl=v-rescale instead of berendsen)?<br>
</blockquote><br></div>Haphazardly changing algorithms for T- and P-coupling without knowing why is a recipe for disaster. Read the literature about each methodology, and choose the one that's appropriate.<br><br>The "problem" regarding box dimensions you pointed out before is related to the fact that you are using isotropic pressure coupling, wherein the box dimensions scale uniformly. That will be the case regardless of which algorithm you use. If the box dimensions change, that's just reality :)<br>
<br>If for some reason you want to fix the box dimensions, use Pcoupl = no.
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">By the way there was a warning after doing grompp, it said "unknown or double left-hand 'bd-temp' in parameter file"<br>
In file.mdp it is<br>bd-temp=300<br>What about this warning related to the problem.......??<br> <br></blockquote><br></div>The .mdp file was generated using an old version of Gromacs. Refer to the manual for changes, and delete that line from the .mdp file.<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Thanks,<br>Jamie
<div class="im"><br><br>On Wed, Jul 22, 2009 at 11:53 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br><br> Jamie Seyed wrote:<br><br> Hi Justin,<br> nstxout=0<br> nstvout=0<br> <br><br> Right, then the .trr file should be empty until the very end, when<br> the last frame should be written. Like I said, probably a<br>
filesystem blip.<br><br> Pcoupl=berendsen<br> Pcoupltype=isotropic<br> <br><br> Note that all of your box vectors are the same at the end. This is<br> probably a consequence of isotropic pressure coupling.<br>
<br> -Justin<br><br> In fact I used the mdp file of /tuto/water and I modified it for<br> PME and v-rescale. But the rest is the same (I am using version<br> 4.0.5)<br> I finished the simulation but I saw file.trr is empty... the<br>
rest seems fine...even file.xtc<br> Thank you,<br> Jamie<br> On Wed, Jul 22, 2009 at 11:32 AM, Justin A. Lemkul<br> <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
</div>
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<div></div>
<div class="h5"> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br><br><br><br> Jamie Seyed wrote:<br>
<br> Dear all,<br> I did a simulation of spce water and every thing seemed<br> ok, when<br> I did mdrun -s file.tpr -o file.trr -c file_out.gro -v -g<br> file.log, I got a file.trr with zero size, but I have<br>
file.xtc<br> that seems fine with VMD. I don't what happened here. Any<br> idea?<br><br><br> What did you set as nstxout and nstvout? Depending on what<br> you set<br> for these parameters, you may not get much in the .trr file; the<br>
final frame should have been written, however. Maybe<br> something went<br> wrong with the filesystem (a blip), and the output was<br> suppressed.<br> I've had that happen when a simulation is finishing and a<br>
.gro file<br> is written, but has nothing in it.<br><br><br> Also I looked at the box size from first file.gro and last<br> file_out.gro..... It shows the box size has been changed a<br>
little bit:<br> first it was 1.86206 1.86206 1.86206<br> finally it is 1.86586 1.86586 1.86586<br> <br> What kind of pressure coupling are you using (if any)?<br>
<br><br> Can someone please kindly make it clear to me why it<br> happened?<br> <br> In general, posting the text of your .mdp file is a good<br> idea. That<br> way, the answers to my questions above are answered :)<br>
<br> -Justin<br><br> Thanks,<br> Jamie<br> ------------------------------------------------------------------------<br><br> _______________________________________________<br>
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<br><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> <<a href="http://vt.edu/" target="_blank">http://vt.edu/</a>> | (540) 231-9080<br>
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<div class="h5"><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>
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