David van der Spoel wrote:
On 3/1/10 5:13 PM, Justin A. Lemkul wrote:
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
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
workaround.
Right, I just included that paper because I came across it when exploring these
thermostat issues myself, and I think they have a really nice discussion of some
of the problems one faces when using thermostats, in general. The paper also
points to a lot of other references that delve more deeply into the underlying
issues.
Hopefully these sorts of links will be useful.
-Justin
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
properly...
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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