I mean here seems to say conserved energy is tilde H [ https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083330.html ]
On Sat, Oct 18, 2014 at 6:44 PM, Johnny Lu <johnny.lu...@gmail.com> wrote: > The conserved energy from g_energy, which I saw someone say is tilde H, > drop more crazily if I use 1s coupling constant. > > On Mon, Oct 13, 2014 at 5:52 PM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > >> Hi, >> >> What is your target observable? What "got worse?" >> >> Mark >> >> On Mon, Oct 13, 2014 at 11:17 PM, Johnny Lu <johnny.lu...@gmail.com> >> wrote: >> >> > The simulation get worse in a new way. >> > >> > I see that thermostat scales velocity and may not fix numerical error in >> > potential energy. >> > >> > On Mon, Oct 13, 2014 at 2:07 PM, Johnny Lu <johnny.lu...@gmail.com> >> wrote: >> > >> > > 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? 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