[gmx-users] Constraint and Temperature Drop in NVE

[Justin Lemkul]

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

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