[gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems

Claus Valka lastexile7gr at yahoo.de
Thu Mar 19 00:02:38 CET 2009


Searching first the gromacs mailing list I could not find an answer to the problem I face.

I would like to know the vaules I have to give to the mdp file where it asks for compressibility.
I have to conduct an NPT simulation using barostat Parrinello-Rahman. My pressure coupling should be anisotropic. The values I have given up to now are:
tau_p                    = 1.0
compressibility          = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5
ref_p                    = 1.0 1.0 1.0 0.0 0.0 0.0

when I try to calculate the elastic constants I get reasonable values for the diagonal elements, yet not good for the off-diagonal. The system I have is a monoclinic one, so giving zeros to xy,xz,yz components is not an option. 
An experimental linear compressibility value I have found out is very close to the value above, so this is why I think I get good values in the diagonal elements.

I have found out many different questions, including one about monoclinic systems. In one of them someone was wondering why he had to put as input the compressibility values, while he is supposed to calculate them from the simulation. As far as the monoclinic system is concerned the question had to to with the components in gromacs derived from the linear experimental values. There was no answer to that.

I have tried some different values myself, for the off - diagonal components and I get either a crash of my simulation of different results for the elastic constants. Is there an algorithm which clearly can point me to the right direction on how to derive the right values? 

Thank you in advance,

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