shaya...@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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