[gmx-users] membrane protein

[Xavier Periole]

On Mon, 17 Dec 2007 09:02:19 +0100
  Jochen Hub <jhub at gwdg.de> wrote:
> Eric Jakobsson wrote:
>> npt, but permit the box to change dimensions independently in the 
>> three directions in response to that component of the virial.
> Does it really matter whether one uses semiisotropic p-coupling or 
>independent coupling in x and y? Are there any examples where semiisotopic 
>p-coupling yields wrong results?

It is obviously more "natural" to let the system adapt in the three
directions independently. It is however often more wise to use a
semiisotropic coupling (x,y responding together to pressure) to avoid
unreasonable/unwanted deformation of the bilayer on one of the x,y
direction.

XAvier

> Jochen
> 
>>
>> At 11:43 AM 12/16/2007, you wrote:
>>> Dear User
>>> I am starting a membrane simulation. Is it advisablr to complete all 
>>> runs in npt or nvt?
>>> Pragya Chohan
>>>  
>>>
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>>
>> ---------------------------------
>> Eric Jakobsson, Ph.D.
>> Professor, Department of Molecular and Integrative Physiology, and of 
>> Biochemistry, and of the Center for Biophysics and Computational Biology
>> Senior Research Scientist, National Center for Supercomputing Applications
>> Professor, Beckman Institute for Advanced Science and Technology
>> 3261 Beckman Institute, mc251
>> University of Illinois, Urbana, IL 61801
>> ph. 217-244-2896  Fax 217 244 9757 
>>
>>
>>
>> ------------------------------------------------------------------------
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> 
> 
> -- 
> ************************************************
> Jochen Hub
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: jhub[at]gwdg.de
> ************************************************ 
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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------