[gmx-users] Use NVT to mimic NVE

[Johnny Lu]

I am not quite in the business of folding/unfolding protein.

On Sun, Oct 12, 2014 at 4:07 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> 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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>
>