I just want something that will patch up the energy lost due to numerical error of NVE simulation of the system ran by mixed precision gromacs, instead of a thermostat.
I hope the velocity rescaling is sufficiently uncorrelated with the motion of the protein. So far, the simulations ran 2.5 ns, and the fluctuation of total energy seems to be within 1% of total energy, with a 100ps or 1ns coupling constant. May be I should try a 10 ns coupling constant, just to see if the simulation would go belly up. On Mon, Oct 13, 2014 at 11:02 AM, Michael Shirts <mrshi...@gmail.com> wrote: > > I guess, if I pick a coupling constant that is just small enough to keep > the > energy conserved, I would get a NVT simulation that is as close as a NVE > simulation as possible. > > > Is this correct? > > Yes, but then at that point the thermostat isn't actually thermostatting. > The Bussi comment is merely to show that his thermostat correctly reduces > to Newton's law in the limit, not that it would be useful to run it in that > limit. > > On Mon, Oct 13, 2014 at 10:28 AM, Johnny Lu <johnny.lu...@gmail.com> > wrote: > > > On page 014101-3, the Bussi paper (http://dx.doi.org/10.1063/1.2408420) > > mentioned: "On the other hand, for coupling constant approaching > > infinity,the Hamiltonian dynamics is recovered." > > Does that means that for a large enough coupling constant, the velocities > > are nearly not rescaled, and the dynamics (like rate of motion) would be > > same as that of NVE? > > > > A larger coupling constant, means a smaller diffusion coefficient in the > > axillary dynamics by equation 6. > > > > While the effects of the velocity rescaling at each step will > accumulate, a > > larger coupling constant means the thermostat perturb less of the > dynamics, > > and the resulting dynamics is closer to a NVE simulation. > > There is no worry that the thermostat would suddenly rescale the dynamics > > every x step, because in the procedure of the thermostat, the velocities > > are rescaled every step, regardless of the coupling constant. > > > > I guess, if I pick a coupling constant that is just small enough to keep > > the energy conserved, I would get a NVT simulation that is as close as a > > NVE simulation as possible. > > > > Is this correct? > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
