[gmx-users] Temperature Coupling and Coupling-Groups

[shayamra at post.tau.ac.il]

Hi Justin,
Thank you very much for your prompt reply. I will make sure to review  
the aforementioned references.

Regards,
-Shay

Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

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