[gmx-users] Use NVT to mimic NVE

[Mark Abraham]

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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