[gmx-users] Use NVT to mimic NVE

[Michael Shirts]

> 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.

Thermostats correct SOME of the artifacts.  It is not always clear which
ones.

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

In SOME cases it may be negligible.  In others, not.  It is very hard to
say.

See our paper linked before http://pubs.acs.org/doi/abs/10.1021/ct400109a
"Effects of Temperature Control Algorithms on Transport Properties and
Kinetics in Molecular Dynamics Simulations"  which covers most short-time
scale effects.

Whether the thermostats that do not affect short time scale properties to
any noticable degree still affect long-time scale properties through some
sort of error accumulation is not known, nor which properties they might
affect.


On Sun, Oct 12, 2014 at 3:07 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> oh, i still mix up things. the numerical error might act as dissipation.
>
> On Sun, Oct 12, 2014 at 3:01 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>
> > 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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