[gmx-users] Use NVT to mimic NVE

[Johnny Lu]

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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