[gmx-users] Constraint and Temperature Drop in NVE

[Johnny Lu]

get that now. It is because the method they talk about for defining the
temperature involves polynomial fitting of position, and computers will
take a long time to do that.

On Wed, Sep 10, 2014 at 1:05 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> 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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>>>
>>>
>>
>