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
