[gmx-users] Constraint and Temperature Drop in NVE

[Johnny Lu]

Somehow I thought about mice, maze, cheese, and food poisoning.

What are the advantages of using multiple thermostat?

On Wed, Sep 10, 2014 at 9:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/10/14 4:29 PM, Mark Abraham wrote:
>
>> Hi,
>>
>> On Wed, Sep 10, 2014 at 5:40 PM, 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
>>> )
>>>
>>>
>> As they note in the discussion, this is not a practical approach for use
>> in
>> a *thermostat* because you need to estimate the time derivative of the
>> position. During the simulation you can only do a one-sided interpolation
>> from previous points, so using such an estimator makes the integration
>> scheme irreversible, which has its own drawbacks. So, an error exists in
>> the momentum-squared-based estimator of the temperature (from
>> finite-time-step size effects), and feeds back into the NVT integration
>> scheme. Whether this matters for the quality of the observables from a
>> given simulation is an open question, but their NVT results suggest that
>> time steps of the usual sizes are not good in combination with multiple
>> thermostats on small-ish systems. They used a Berendsen thermostat, which
>> is known to sample the wrong ensemble, so their NVT results may not be
>> quantitatively accurate, but offhand I'd expect to observe the trend they
>> see.
>>
>> Naturally, one could write code to do two-sided interpolation as they do
>> there and so get a reliable temperature estimate in post-processing, but
>> nobody has bothered to do that. BTW, GROMACS does report the conserved
>> quantity for all integration schemes that have one.
>>
>> Mark
>>
>> 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
>>>
>>
> To this point, the tutorials aim to provide simple, robust systems with
> reproducible results that use "common" practices.  As I note fairly
> prominently in all of my tutorials, no one should view the .mdp files as
> definitively correct for anything you might want to do.  They work in their
> intended context and that is the main point.  Multiple thermostats are
> common practice, though recent literature has of course indicated that
> different approaches may be better.  Strictly speaking, multiple
> thermostats are a violation of equipartition of energy, but there were
> practical reasons why they were used.
>
> Perhaps it should also be said that tutorials linked from the Gromacs page
> are provided as a convenience to users and are not intended as an
> endorsement by the Gromacs developers.  The tutorials are the
> responsibility of their individual authors.  Of course, I realize that in
> my case, I am both... ;)
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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