[gmx-users] Constraint and Temperature Drop in NVE

[Mark Abraham]

Hi,

It's impossible to say anything in the absence of a full description of the
system and .mdp file - expecting good conservation can be a fool's errand.
You could
a) investigate the effect of time step on the difference in the observed
temperature
b) investigate the effect of the restraint strength constant on the
temperature difference (it could be too large for the time step)
c) try double precision (to see if the drift is intrinsic or due to
accumulated rounding imprecision)
d) assess which of the approximations you are making (drift from finite
time step/model/implementation, static point charges, broken ergodicity,
etc.) dominates the quality of your model physics.

And consider that the measurement of temperature from momentum (as in
GROMACS) is intrinsically flawed - see
https://www.deshawresearch.com/publications/Equipartition%20and%20the%20Calculation%20of%20Temperature%20in%20Biomolecular%20Simulations.pdf

Mark


On Wed, Sep 3, 2014 at 6:21 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> I try the following:
>
> 0. Minimization
> 1. NVT (100,000 steps of 2fs, 300K)
> 2. NPT (100,000 steps of 2fs, 300K, V-rescale thermostat)
> 3. NPT (5000 steps of 2fs, 308K, V-rescale thermostat)
> 4. 9 x NVE (each 32768 steps of 0.75 fs)
> 5. go to step 3.
>
> I plan to get rid of the first of nine NVE steps, as an NVE equilibration
> step.
>
> At 0.75 fs, the total energy drop was about 0.03% per NVE step.
>
> Will that be fine? I am a bit worry that step 3 is too short.
> I pick 308K because last time when I choose 300K for step 3, step 4 drops
> to 292 K.
> I hope that the NVE will be about 300K.
>
> May be I should look at the .edr file of step 3.
>
> Thanks.
>
>
> On Wed, Sep 3, 2014 at 11:54 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>
> > reading this post in maillist again:
> >
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-May/071225.html
> >
> > I think that is exactly the same problem.
> >
> >
> > On Wed, Sep 3, 2014 at 10:24 AM, Johnny Lu <johnny.lu128 at gmail.com>
> wrote:
> >
> >> Hi.
> >>
> >> After equilibrating with NVT (for 10,000 steps of 2fs) and then NPT
> >> (10,000 steps of 2fs with V-rescale thermostat at 300K), when I run NVE
> >> (0.5fs timesteps) with a harmonic restraint with force constant
> 4184kJ/mol
> >> rad^2, the temperature then fluctuate around 292 K (
> >> http://oi60.tinypic.com/sni5at.jpg) in gromacs 4.6.6.
> >>
> >> When I instead run NVE with same setting except without the constraint
> >> after the two equilibration steps, the temperature stays around 300K.
> >>
> >> What is the cause of this drop of temperature to 292K?
> >>
> >> Thanks again.
> >>
> >>
> >>
> >
> --
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