rabab,<br><br>justin mentioned the *gro file saved at the end of the simulation - the last line contains the box dimensions.<br><br>you can extract them with g_energy:<br><div style="margin-left: 40px;"><span style="font-family: courier new,monospace;">g_energy -f your_edr_file -o your_output_file</span><br>
</div>and then selecting:<br><div style="margin-left: 40px;"><span style="font-family: courier new,monospace;">Box-X</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">Box-Y</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">Box-Z</span><br></div><br><br>good luck,<br>igor<br><br clear="all"> Igor Marques<br>
<br><br><div class="gmail_quote">On Mon, Jul 25, 2011 at 5:07 PM, Rabab Toubar <span dir="ltr"><<a href="mailto:rtoubar@yahoo.com">rtoubar@yahoo.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Thanks Justin for your reply. But what is the extension of the output coordinate file. And for the .edr file it failed to open in windows; how can I possibly view it<br>
<br>
Thanks<br>
Rabab Toubar<br>
<br>
<br>
<br>
--- On Mon, 7/25/11, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
<br>
> From: Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
> Subject: Re: [gmx-users] water box size from output files<br>
> To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
> Date: Monday, July 25, 2011, 11:15 AM<br>
<div><div></div><div class="h5">><br>
><br>
> Rabab Toubar wrote:<br>
> > Hi<br>
> ><br>
> > I was wondering if there is a way to determine the<br>
> water box size from the output files after the simulation<br>
> run is over<br>
> ><br>
><br>
> Box vectors are printed to the output coordinate file<br>
> (final snapshot) and can be extracted from along the<br>
> trajectory from the .edr file.<br>
><br>
> -Justin<br>
><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>
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</div></div></blockquote></div><br>