I would use grep and cut to take the atom numbers of the residues I want to restrain and direct them into an index file with [res_sol] at the top. Then use genrestr to generate restraints for these atoms using the -n option. Then conditionally include this restraint file (.itp file) in my topology when you use -DPOSRES_res_sol (or whatever just make it match what's in the top file) in your mdp file.
Thats how I would put position restraints on parts of my system. I think different constraints are answered here too :) Good luck, Oliver On 2 December 2010 08:21, David Rodríguez <[email protected]>wrote: > 2010/12/2 Mark Abraham <[email protected]> > > On 2/12/2010 12:51 PM, Guido Polles wrote: >> >>> Hi, >>> I know it looks a little bit strange, but i was trying to restrain >>> just some water in my system. >>> Now, if i put something like >>> [ position_restraints ] >>> ; i funct fcx fcy fcz >>> 1 1 1000 1000 1000 >>> I put restraints on all the molecules. >>> >> >> Yes, that directive will pertain to all the molecules that have that [ >> moleculetype ]. I'm not sure if you only want position restraints on some of >> your water molecules. >> >> >> I thought about a turnaround, just making a second water molecule >>> type, but now complains about using more than one settle type. >>> Is there any other way to do it? >>> >> > Guido, > You may find this thread useful: > http://lists.gromacs.org/pipermail/gmx-users/2010-September/054087.html > > >> And if I follow the "Suggestion: change the least use settle >>> constraints into 3 normal constraints" I have to worry about some kind >>> of huge loss in performance? >>> >> >> I would expect the non-settle waters to use the solvent-optimized loops in >> the normal way, so there should be no difference in execution time between >> the unrestrained all-settle simulation and the partly-restrained >> party-settled simulation. Obviously, this is straightforward to test. >> >> Mark >> >> -- >> 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 >> > > > > -- > David Rodríguez Díaz, PhD Student > Fundación Pública Galega de Medicina Xenómica (SERGAS) > Web page: http://webspersoais.usc.es/persoais/david.rodriguez.diaz > > -- > 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 >
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