[gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems
Berk Hess
gmx3 at hotmail.com
Thu Mar 19 10:23:27 CET 2009
Hi,
If you have a liquid system (no off-diagonal elasticity), you should not use full anistropic pressure coupling.
If you have a solid system (for instance a crystal), you will have an elastic shear stress response
and you can determine and use off-diagonal compressibility values.
You need the compressibility values to set the time scale of the pressure coupling.
The compressibility does not affect any thermodynamic quantity, only the dynamics.
The compressibility always occurs as a product with 1/tau_p.
If you want to determine them from a simulation, you need a reasonable initial guess
for the compressibility and you can use a large tau_p to be on the safe side
with the actual coupling time.
Berk
Date: Wed, 18 Mar 2009 16:02:38 -0700
From: lastexile7gr at yahoo.de
To: gmx-users at gromacs.org
Subject: [gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems
Hello,
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,
Nikos
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