[gmx-users] Constraint and Temperature Drop in NVE

[Johnny Lu]

Reading that paper again, I saw it says that deviation from the
equipartition (but not the generalized-equipartition) signifies truncation
error.


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

> 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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>>
>>
>