[gmx-users] Variation of angles of simulation cell - regd

ramesh cheerla 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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