Thanks for your answer. How can I tell which ones I should restrain? all no-H atoms? in most general situations.
lina ________________________________________ From: [email protected] [[email protected]] on behalf of Justin A. Lemkul [[email protected]] Sent: Wednesday, September 22, 2010 11:15 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Position Restraints #ZHAO LINA# wrote: > Hi, > > When I used the genrestr to get the posre.itp specially, > I found it set all atom to be applied to. > Is that okay? How could I figure out which ones should not be set to. > > A little naive questions, but I do do not know. The answer depends on your needs. When running genrestr without an index file, you can choose from any of the default groups. If you provide an index file, any group can be chosen. The default behavior of pdb2gmx is to generate a posre.itp file that restrains all heavy (non-H) atoms. You can do the same with genrestr if you want, but again, the atoms you want to restrain depend on your goals. -Justin > > Thanks with regards, > > lina > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
