On Thu, May 30, 2013 at 12:31 PM, James Starlight <jmsstarli...@gmail.com>wrote:
> Also some questions about corrections in the mdp besides the time-step file > which should be included with the VS. > > 1) What constrains algorithm should I use ? > typically I use > ; Bond parameters > constraint_algorithm = lincs ; holonomic constraints > constraints = all-bonds ; all bonds (even heavy atom-H bonds) > constrained > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > At high parallelization, all-bonds becomes limiting, which can be mitigated with changed lincs parameters. See manual. 2) Should I vary tau_t constant assuming that I use SD integrator as the > thermostat ( I'm using 2 ps ) ? > Don't know. Mark > > 2013/5/30 James Starlight <jmsstarli...@gmail.com> > > > 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 > -- 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
