Francesca, Yes I suppose this is good aproach for the generation of position restricktions on the desired atoms. But I want to restrain the distance between selected pairs of atoms ( e.g between C-alpha- C-alpha atoms of two different residues).
Also I want to restrain some dihedral angles in the desired rotameric forms. In literature I've found that peple have dome the same things in Gromacs but I could not find detailed algorithm of such methodology :( James 12 марта 2012 г. 18:05 пользователь francesca vitalini < francesca.vitalin...@gmail.com> написал: > 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 >
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