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

Erik Lindahl lindahl at sbc.su.se
Tue Jun 20 10:46:17 CEST 2006


On molecular levels, 1 and 0 atm are virtually identical unless you  
are doing a millisecond simulation. The fluctuations will be at least  
+-500 atm. Thus, you'll almost certainly be fine.

As for off-diagonal elements, if you don't want the box shape to  
change you need to set the _compressibility_ to zero there.



On Jun 19, 2006, at 11:55 PM, 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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