Hi, You also have to spend a sufficient amount of thought on the question whether an approach like that will give you what you're after. It's not going to sample a relevant ensemble and you're disabling the long range correlations that may be of influence on ligand binding.
Cheers, Tsjerk On Wed, Mar 17, 2010 at 9:01 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Anna Marabotti wrote: >> >> Dear gmx-users, >> I'd like to perform a molecular dynamics simulation on a protein-ligand >> complex, in such a way that only residues belonging to the active site can >> move, whereas the rest of the protein is kept fixed. I searched for some >> information about how to do it with GROMACS, but I didn't find anything. >> Could anybody give me some suggestions about this subject, please? > > You could create a custom posre.itp (using genrestr) to restrain whatever > atoms you choose, but it won't speed up your calculations in any way, if > that's what you're after. You could also specify freezegrps in the .mdp > file, which requires a custom index group; it may be more difficult to use > this setup based on the types of exclusions that would be necessary within > whatever is frozen. > > -Justin > >> Many thanks in advance and regards. >> Anna >> __________________________________________________________________ >> Anna Marabotti, Ph.D. >> Laboratory of Bioinformatics and Computational Biology >> Institute of Food Science - CNR >> Via Roma, 64 >> 83100 Avellino >> Phone: +39 0825 299651 >> Fax: +39 0825 781585 >> E-mail: amarabo...@isa.cnr.it <mailto:amarabo...@isa.cnr.it> >> Skype account: annam1972 >> Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm >> "If you think you're too small to make a change, try sleeping with a >> mosquito" >> > > -- > ======================================== > > 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 gmx-us...@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
