[gmx-users] Temperature Coupling and Coupling-Groups

David van der Spoel spoel at xray.bmc.uu.se
Mon Mar 1 17:47:06 CET 2010

On 3/1/10 5:13 PM, Justin A. Lemkul wrote:
> 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

That's interesting, thanks for putting this together Justin.
I haven't read the paper from the Tavan group completely, but I don't 
think they truly solve the problem, do they? It reads more like some 

The origin of the problem is the lack of coupling between the different 
degrees of freedom, and as such one would expect united atom force 
fields to show this effect to a larger degree than all-atom force 
fields. It could also be that the use of constraints makes that the 
effective number of degrees of freedom per atom is different for 
proteins and water. It seems that this still hasn't been investigated 

> 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

David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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