[gmx-users] Use NVT to mimic NVE

[Johnny Lu]

Sorry that I misunderstood your post.

Can compensating energy lost caused by numerical error with thermostat
cause error in the probability distribution of thermodynamic variables and
distribution of conformations?

Below is just a guess. I don't understand the fluctuation dissipation
theorem enough at this point.

I would guess so.. unless the fluctuation of the velocity of the atom
doesn't follow maxwell-Boltzmann distribution (I guess that can happen in a
crystal made of harmonic oscillator of a single frequency, or if some part
of the protein has low degree of freedom. This is a flaw found in
nose-hover thermostats.)

Otherwise, some thermostats already try to provide the correct fluctuation,
so that the distribution of thermodynamic variables is correct (as in
fluctuation-dissipation theorem). If we use thermostats, the thermostats
will correct the energy drop/raise caused by numerical error (which acts as
a fluctuating source/sink that may not even follow the normal
distribution), without causing additional artifacts.

Regardless, thermostats causes artifacts, especially in dynamics and rates.

On Sun, Oct 12, 2014 at 2:07 PM, Michael Shirts <mrshirts at gmail.com> wrote:

> > The point was that if the energy leaves the system, then the system
> is never in equilibrium. Not vice versa, please.
>
> This is incorrect logic.  f there are errors in the integrator, then
> F=gradient of the potential is not true. If that is not true, energy is not
> conserved, and energy can leave or enter the system.
>
>
> On Sun, Oct 12, 2014 at 1:58 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>
> wrote:
>
> > The point was that if the energy leaves the system, then the system is
> > never in equilibrium. Not vice versa, please.
> >
> >
> >
> > Dr. Vitaly V. Chaban
> >
> > Виталий Витальевич ЧАБАН
> >
> >
> > On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu <johnny.lu128 at gmail.com>
> wrote:
> > > Why non-equilibrium can cause lost of total energy in NVE simulation?
> > > (baring the case that the non-equilibrium causes very large values that
> > > causes over flow / getting out of the stable range of algorithms of
> > > gromacs).
> > >
> > > A closed system should have constant energy, regardless of whether it
> is
> > at
> > > equilibrium.
> > >
> > > I guess people use the word "converge" instead of equilibrium in
> > molecular
> > > dynamics simulation of protein, possibly because the simulation may
> never
> > > reach equilibrium with current computing power.
> > > http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b
> > >
> > > I may try older version of gromacs and/or not using constraint, after
> > > checking the bug list and performance. I had never thought about that
> > route.
> > >
> > >
> > >
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