Message: 6 Date: Tue, 16 May 2006 23:02:15 +1000 From: Mark Abraham <[EMAIL PROTECTED]> Subject: Re: [gmx-users] 2 beginner?s questions To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Sampo Karkola wrote: > Hi, > > also VMD is quite handy. You'll need pdb's for VMD, too. Not true. VMD eats at least .gro, .g96, .trr and .xtc as well as .pdb and a whole pile of others. M.F.: Indeed - VMD takes every gromacs formats Just take care about the terminal residials - sometimes VMD doesn't treat them properly. In this case just use the 'atomselect' option to select the whole molecule for a reperesentation/analysis (via the atom indexes). It is also a good idea to remove periodicity (with gromacs tools) BEFORE analysing your trajectory with VMD. But as a whole - the VMD could be a good choice. Maxim. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
