<div>Thank you Justin,</div>
<div> </div>
<div>But how I can prevent from that (filesystem blip) to happen. Also May I change Pcoupl= Parrinello-rahman instead of berendsen (has it any effect?? since I have changed Tcoupl=v-rescale instead of berendsen)?</div>
<div>By the way there was a warning after doing grompp, it said "unknown or double left-hand 'bd-temp' in parameter file"</div>
<div>In file.mdp it is </div>
<div>bd-temp=300</div>
<div>What about this warning related to the problem.......??</div>
<div> </div>
<div>Thanks,<br>Jamie<br><br></div>
<div class="gmail_quote">On Wed, Jul 22, 2009 at 11:53 AM, 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">Hi Justin,<br>nstxout=0<br>nstvout=0<br> <br></blockquote><br></div>Right, then the .trr file should be empty until the very end, when the last frame should be written. Like I said, probably a filesystem blip.<br>
<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Pcoupl=berendsen<br>Pcoupltype=isotropic<br> <br></blockquote><br>Note that all of your box vectors are the same at the end. This is probably a consequence of isotropic pressure coupling.<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im">In fact I used the mdp file of /tuto/water and I modified it for PME and v-rescale. But the rest is the same (I am using version 4.0.5)<br>I finished the simulation but I saw file.trr is empty... the rest seems fine...even file.xtc<br>
Thank you,<br>Jamie<br></div>
<div>
<div></div>
<div class="h5">On Wed, Jul 22, 2009 at 11:32 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> Dear all,<br> I did a simulation of spce water and every thing seemed 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 file.xtc<br>
that seems fine with VMD. I don't what happened here. Any idea?<br><br><br> What did you set as nstxout and nstvout? Depending on what 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 something went<br> wrong with the filesystem (a blip), and the output was suppressed.<br> I've had that happen when a simulation is finishing and a .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><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 happened?<br> <br><br>
In general, posting the text of your .mdp file is a good idea. That<br> way, the answers to my questions above are answered :)<br><br> -Justin<br><br> Thanks,<br> Jamie<br> <br> ------------------------------------------------------------------------<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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