[gmx-users] Which ensemble for membrane proteins?

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 30 15:14:57 CEST 2008

sudheer babu wrote:
> Hi everybody,
>                    I have read one review article( 
> dissertations.ub.rug.nl/FILES/faculties/science/1998/d.p.tieleman/c1.pdf 
> <http://dissertations.ub.rug.nl/FILES/faculties/science/1998/d.p.tieleman/c1.pdf> 
> ) about membrane proteins tells about POPC alone simulations should 
> run in NPT but not in NVT conditions. Regarding protein run in both 
> some time NPT remain time NVT, till now fine . But when protein 
> inserted into POPC in which ensemble conditions have to follow? Can 
> anyone knows please tell me
> Thanks in advance.

I would continue searching the literature.  In the linked article you 
provide, it is mentioned that NVT can induce artefacts, so that is 
probably a good reason to avoid it for any system containing a lipid 
bilayer.  I have never seen a published membrane protein paper that used 
NVT, although I certainly haven't read them all!

Another good article to read (among many) is:  Kandt, et al. (2007) 
Methods. 41: 475-488.  Anything else by Tieleman and associates is good, 
so starting your search there would be a reasonable choice.


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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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