Hi Myunggi Yi,<br><br>In addition, it may help if you give some examples: link the structure file, the topology file, and some sample images highlighting the point your trying to make. Apparently, leaving us guessing doesn't help.
<br><br>Tsjerk<br><br><div class="gmail_quote">On Jan 16, 2008 12:10 AM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d">Myunggi Yi wrote:<br>> Thank you.<br>><br>> I know general setup to run a simulation, and I'm running one.<br>> As you see the title, I have problem with image.<br><br></div>Well that was a dozen emails ago and we've talked about many topics
<br>since. You'll get nowhere fast by assuming that the people you're asking<br>for help have the whole email exchange memorized... they have their own<br>problems. To get effective help, describe things fully, and if you need
<br>to refer back to something, go and get a URL to the mailing list<br>archives on the GROMACS webpage. This may seem onerous, but you're the<br>one trying to get free help, so you maximise your chances by making life
<br>easier on the people who might give it to you.<br><div class="Ih2E3d"><br>> I'm getting broken lipid in the trajectory.<br><br></div>You're not. mdrun doesn't write broken molecules if they were whole in
<br>the topology. Your visual representation might have them crossing PBC<br>boundaries in a way that might make them look broken, however. There are<br>many ways to adjust your visual representation, however.<br><div class="Ih2E3d">
<br>> Would you let me know how to avoid this?<br><br></div>As someone else has already suggested, judicious use of trjconv and the<br>.gro file you use with VMD are needed here. Read the man page for<br>trjconv and experiment to find what works for whatever your trying to do.
<br><div class="Ih2E3d"><br>> Do I need special setup?<br><br></div>No<br><div><div></div><div class="Wj3C7c"><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
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Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8 <br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931 <br>F: +31-30-2537623