[gmx-users] Constraint and Temperature Drop in NVE

[Johnny Lu]

hmm. If that is the case, I have two questions.
1. Why gromacs doesn't adopt the method of measuring temperature as
described in the JCTC paper?
    (
https://www.deshawresearch.com/publications/Equipartition%20and%20the%20Calculation%20of%20Temperature%20in%20Biomolecular%20Simulations.pdf
)

2. As the paper mentioned that using two thermostats can cause hot solvent
cold solute problem for the timesteps that we commonly use, why do your
lysozyme tutorial still use two thermostats?
    (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/nvt.mdp
)

Thank you.


On Wed, Sep 3, 2014 at 4:07 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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