[gmx-users] Temperature Coupling and Coupling-Groups

[Justin A. Lemkul]

shayamra at post.tau.ac.il wrote:
> Greetings dear Gromacs users,
> 
> I would like to create a membrane-protein simulations (popc + protein, 
> water, Na Cl ions, using Berendsen thermostat) and I am not sure which 
> coupling-groups I should use.
> For example, why not couple the whole system together?
> 
> I do realize that this is a large request on this type of mailing list. 
> I will also be happy to receive references to relevant literature.

Most reports in the literature describe protein, lipids, and solvent+ions in 
separate groups.  The reasons for not coupling the whole system together are 
well-documented, and as a matter of fact, I just updated the Gromacs wiki this 
weekend to point to several papers describing this phenomenon:

http://www.gromacs.org/Documentation/Terminology/Thermostats

There are also numerous threads in the list archive on this topic, likely with 
other references that I did not link.

-Justin

> 
> Thanks in advance,
> -Shay
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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