[gmx-users] Constraint and Temperature Drop in NVE

[Justin Lemkul]

On 9/10/14 9:45 PM, Johnny Lu wrote:
> Somehow I thought about mice, maze, cheese, and food poisoning.
>
> What are the advantages of using multiple thermostat?
>

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-September/075002.html

There are many other posts in the archive with more information.  It's not so 
much an "advantage" as it is a tactic to overcome problems in nonbonded schemes, 
which are greatly reduced when using PME.

-Justin

> 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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-- 
==================================================

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

==================================================