I think you can make an index file using make_ndx where you specify the atoms you want to restraint. Hope this can help. Francesca
2012/3/12 James Starlight <jmsstarli...@gmail.com>: > Dear Gromacs users! > > > I want to perform constrained MD simulation of my protein with inclusion of > some experimental restraints. > > > 1) I found that genrest cpmmand could be usefull for the generation of the > distance restrictions wich I could use in my constrined simulation. > > Also in manual I've found that command like > > genrestr -f b2ar.gro -disre -index.ndx -o test.itp > > will produce some distance restricted matrix of the whole groups presented > in the index.ndx file. > > So how I could select to contrain selected residues within selected distance > by means the index file? E.g I've manually point out 2 residues in > index.ndx. I waant to preserve between that residues some desired distance D > wich I've obtaine from the experimental data. How I could do it via genrestr > and waht addition flags should I use for that purpose ? > > > 2) Is there any way to apply gradually the desired dist.resrs during MDrun > to prevent some artifacts in my system wich would occur due to the rapid > application of the dis.res ( e.g in cases where the conformation of the > started structure and that wich I'd obtained fter application of the > restrains are slightly different)? > > Thanks for help, > > > James > > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
