[gmx-users] off-diagonal of the tensor for pressure coupling should be zero??

Arneh Babakhani ababakha at mccammon.ucsd.edu
Tue Jun 20 00:07:33 CEST 2006

Sunjoo, is there a particular reason why you want to you anisotropic 
pressure coupling? (I recently tried this myself, on a DMPC bilayer). 
Some of the key membrane physical properties (like thickness, area per 
lipid, order parameters) were distorted and did not agree with 
experimental evidence. So I went with semiisotropic pressure coupling 
instead, that was much better.


이 선주 wrote:
> Dear Gromacs people
> I am trying to run NPT simulation on a bilayer and want to know right 
> setup to use anisotropic pressure coupling.
> I have seen two different cases of reference pressure.
> Some people use 1 atm for off-diagonals (xy, yz, zx directions) but 
> other use 0 atm.
>> From Erik's answer, I could see that if the system is not allowed to 
>> deform 
> to triclinic from rectangular shape, then the last three reference 
> pressures should be zero.
> Before I saw his answer, I already ran MD simulation with 1 atm for 
> the off-diagonal of the pressure tensor. I have not seen any 
> particular problem with this setup.
> Can anyone tell me what problem might have been caused becuase of the 
> pressuring coupling to the off-diagonal directions?
> Thank you
> Sunjoo
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