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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