[gmx-users] Use NVT to mimic NVE

[Johnny Lu]

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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