[gmx-users] Use NVT to mimic NVE

[Johnny Lu]

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.abraham at 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.lu128 at 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.lu128 at 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 <mrshirts at 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.lu128 at 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?
> > >> > --
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