On 9/09/2012 11:41 PM, ramesh cheerla wrote:
Dear Gromacs users,
Recently I have converted each frame of the
trajectory to a pdb file using gromacs tool "g_trjconv" and then
have extracted angles from the CRYST1 record of pdb file, to see how
they are varying in simulation. By doing so I have observed that my
box angles alpha and gamma are not at all varying through out the
simulation these values are remains at "90" degrees and there is a
change in beta value.
I have used "triclinic box" for simulations of my system with angles
alpha = 90, beta=120 and gamma=90 and have used "NPT" ensemble with
following options in mdp file "pcoupltype = anisotropic and
ref_p = 1.0 1.0 1.0 0.0 0.0 0.0 "
here my questions are:
1) What might be the probable reason for constant values of alpha and
beta ( why these values are not changing).
See 7.3.15, which of course you read before using anisotropic coupling.
You're making life hard by not giving your full .mdp file, because
you're leaving us to guess about your compressibilities. Do summarise,
but don't exclude. :-) Presumably your choices are consistent with a
monoclinic box staying that way.
2) Am I following correct protocol to extract angles, or Is there any
better way to extract angles from trajectory.
If you want lattice parameters, that's probably the best way to get them.
3) Am I using correct options in .mdp file.
Can't tell.
Mark
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