2010/12/2 Mark Abraham <mark.abra...@anu.edu.au> > 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 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 > -- David Rodríguez Díaz, PhD Student Fundación Pública Galega de Medicina Xenómica (SERGAS) Web page: http://webspersoais.usc.es/persoais/david.rodriguez.diaz
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