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 2) Should I vary tau_t constant assuming that I use SD integrator as the thermostat ( I'm using 2 ps ) ? 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
