[gmx-users] Use NVT to mimic NVE

[Johnny Lu]

Thank you for pointing me to that paper. I took a quick look of it
yesterday.
Would the results in the paper stay the same, if the side chain rotations
of a protein is investigated?

On Sun, Oct 12, 2014 at 3:30 PM, Michael Shirts <mrshirts at gmail.com> wrote:

> > 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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