[gmx-users] Use NVT to mimic NVE

[Johnny Lu]

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.lu128 at 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.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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