<div>Hi Justin,</div>
<div>nstxout=0</div>
<div>nstvout=0</div>
<div> </div>
<div>Pcoupl=berendsen</div>
<div>Pcoupltype=isotropic</div>
<div> </div>
<div>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</div>
<div> </div>
<div>Thank you,</div>
<div>Jamie<br></div>
<div class="gmail_quote">On Wed, Jul 22, 2009 at 11:32 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">Dear all,<br>I did a simulation of spce water and every thing seemed ok, when I did mdrun -s file.tpr -o file.trr -c file_out.gro -v -g file.log, I got a file.trr with zero size, but I have file.xtc that seems fine with VMD. I don't what happened here. Any idea?<br>
</blockquote><br></div>What did you set as nstxout and nstvout? Depending on what you set for these parameters, you may not get much in the .trr file; the final frame should have been written, however. Maybe something went wrong with the filesystem (a blip), and the output was suppressed. I've had that happen when a simulation is finishing and a .gro file is written, but has nothing in it.
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Also I looked at the box size from first file.gro and last file_out.gro..... It shows the box size has been changed a little bit:<br>
first it was 1.86206 1.86206 1.86206<br>finally it is 1.86586 1.86586 1.86586<br> <br></blockquote><br></div>What kind of pressure coupling are you using (if any)?
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Can someone please kindly make it clear to me why it happened?<br> <br></blockquote><br></div>In general, posting the text of your .mdp file is a good idea. That way, the answers to my questions above are answered :)<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<br> <br><br>------------------------------------------------------------------------<br><br>
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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><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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