On Thu, May 30, 2013 at 12:17 PM, James Starlight <jmsstarli...@gmail.com>wrote:
> Mark, > > thanks for advise. As I understood for the usage of virtual sites in > typical protein-water system I should > (1) define all hydrogens as the virtual atoms (2) increase atom masses of > the hydrogens presented in the water, Not applicable if you are using a rigid water model. > COOH NH2 OH and SH as well as polar > groups (3) make virtual sites for the angles and dihedrals of peptide bond > as well as sidechains. > > Also I've noticed that (1) and (2) can be done with the pdb2gmx with > options -vsite and -heavyh respectfully. From this point its not quite > clear for me > (1) should I make some corrections in topology for dihedrals? In the manual > 6.7 I've found some suggestions for the dihedrals of the different > functional groups. > Generally, use what pdb2gmx will generate and don't worry further. I have heard the thought expressed that the aromatic constructions are not good in practice, but I don't know any details. > (2) should I define VSITES for solvent molecules filled into the box by > the genbox ? > (3) As I understood the inclusion of the VSITES for hydrogens would allow > me to increase timestep up to 5-8fs. What possible negative side-effects > of the inclusion of VSITES might occur in simulation ? > The vsites are generally fine. See paper referenced there for some details. Mark > > James > > 2013/5/30 Mark Abraham <mark.j.abra...@gmail.com> > > > Manual 6.7? > > > > > > On Thu, May 30, 2013 at 7:05 AM, James Starlight <jmsstarli...@gmail.com > > >wrote: > > > > > Dear Gromacs users! > > > > > > In some discussions I've noticed that people told about usage of > virtual > > > sites which allow to increase time step of the simulation of such > > systems. > > > >From manual and tutorial its not quite understand for me how with > > > inclusion > > > of such dummy atoms (which can be used to reduce number of atoms of the > > > some solvent-like molecule or to mimic electron pairs in the water for > > > instance) influence on time-step can be achieved ? > > > > > > > > > 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 > > > -- > 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
