Hi Myunggi Yi, 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.
Tsjerk On Jan 16, 2008 12:10 AM, Mark Abraham <[EMAIL PROTECTED]> wrote: > Myunggi Yi wrote: > > Thank you. > > > > I know general setup to run a simulation, and I'm running one. > > As you see the title, I have problem with image. > > Well that was a dozen emails ago and we've talked about many topics > since. You'll get nowhere fast by assuming that the people you're asking > for help have the whole email exchange memorized... they have their own > problems. To get effective help, describe things fully, and if you need > to refer back to something, go and get a URL to the mailing list > archives on the GROMACS webpage. This may seem onerous, but you're the > one trying to get free help, so you maximise your chances by making life > easier on the people who might give it to you. > > > I'm getting broken lipid in the trajectory. > > You're not. mdrun doesn't write broken molecules if they were whole in > the topology. Your visual representation might have them crossing PBC > boundaries in a way that might make them look broken, however. There are > many ways to adjust your visual representation, however. > > > Would you let me know how to avoid this? > > As someone else has already suggested, judicious use of trjconv and the > .gro file you use with VMD are needed here. Read the man page for > trjconv and experiment to find what works for whatever your trying to do. > > > Do I need special setup? > > No > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
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