[gmx-users] Constraint and Temperature Drop in NVE

[Johnny Lu]

sorry, i mean the lysozyme tutorial that i found there...

On Wed, Sep 10, 2014 at 11:40 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> 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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