Mark, could you also provide me with some examples when usage of VS could give artifacts in simulations ? In particular I'm interesting in usage of VS on hydrogens with membrane proteins.
James 2013/6/1 James Starlight <jmsstarli...@gmail.com> > Thanks for so detailed explanation! > > I've also forced with the problem of barostat during simulation of my > membrane protein with N-H chains ( see adjacent topic). I'll be also very > thankful for you suggestion in that case too. > > James > > > 2013/6/1 Mark Abraham <mark.j.abra...@gmail.com> > >> On Fri, May 31, 2013 at 5:19 PM, James Starlight <jmsstarli...@gmail.com >> >wrote: >> >> > 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 ) >> > >> >> You're integrating forces calculated at one instant and assuming they are >> applicable over a finite time period. Obviously this is an approximation, >> and it gets worse with longer time step. The worse approximation means the >> sampling is from a shadow Hamiltonian that is even further from the real >> one. P-R is not very stable if the sampling is not from equilibrium, so >> probably the change suggested in the warning helps keep P-R working. >> >> The absence of the simulation crashing is not a suitable proxy for >> assuming >> there are no problems. You should compare observables with those from >> conservative parameter sets and see whether differences exist. >> >> Mark >> -- >> 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
