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, 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. (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 ? 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
