<div>Thank you very much.</div>
<div>Trjconv works fine.</div>
<div> </div>
<div>Marian<br><br></div>
<div class="gmail_quote">On Mon, Mar 9, 2009 at 1:10 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>Mark Abraham wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">----- Original Message -----<br>From: Nuno Azoia <<a href="mailto:nazoia@det.uminho.pt" target="_blank">nazoia@det.uminho.pt</a>><br>
Date: Monday, March 9, 2009 21:52<br>Subject: Re: [gmx-users] editconf and genbox using method<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hello!<br><br>Your box isn't rectangular. Your problem is just VMD display the gro<br>file with a rectangular shape. If you need to see your system properly<br>
try to transform your .gro file in a .pdb file first, using trjconv.<br><br>Try trjconv -h to see the options<br></blockquote><br>I don't believe this is correct. That would be a bizarre thing for VMD to do. Much more likely is that editconf actually selected a rectangular box, genbox filled it, and VMD is displaying what's in the file.<br>
<br></blockquote><br></div>Actually, I've found trjconv to be necessary. VMD indeed shows a rectangular box for my dodecahedral systems, if I have not used trjconv -pbc mol -ur compact.<br><br>The transformation to .pdb, however, is unnecessary. The .gro file can be processed in the same way.<br>
<br>-Justin
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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<br></blockquote><br></div>-- <br>========================================<br><br>Justin A. Lemkul<br>Graduate Research Assistant<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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