[gmx-users] Variation of angles of simulation cell - regd
rameshgromacs at gmail.com
Sun Sep 9 15:41:59 CEST 2012
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).
2) Am I following correct protocol to extract angles, or Is there any
better way to extract angles from trajectory.
3) Am I using correct options in .mdp file.
Thank you in advance.
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