3) Also I've already performed small simulation with the time step 5 fs (defining virtual sites by means of pdb2gmx -vsites and introducing heavy hydrogens. I've not observed any errors during my simulation. When I've tried to increase dt up to 7 fs I've obtained warnings according to that I should increase tau_p (from 2 ps with Parinello coupling). How tau_p is relevant to the timestep and when I could obtain more information about such constants ? E.g if i increase tau_p doest it means that I provide weaker coupling to the system with pressure bath ? (higher constant- higher relaxation times )
James 2013/5/30 James Starlight <jmsstarli...@gmail.com> > 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