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 <jalem...@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.lu...@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
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Justin A. Lemkul, Ph.D.
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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