[gmx-users] Variations of angles in a triclinic box
antonio.pizzirusso80 at gmail.com
Wed Apr 22 16:15:41 CEST 2015
Dear Gromacs users,
Recently I have used NPT ensemble with the following options in mdp file:
Pcoupl = berendsen
Pcoupltype = anisotropic
tau-p = 1.0 1.0 1.0 0.0 0.0 0.0
compressibility = 1.0e-5 1.0e-5 1.0e-5 0.0 0.0 0.0
ref-p = 1.033 1.033 1.033 0.0 0.0 0.0
for simulating a triclinic box (where alpha, beta and gamma differs thus
from 90 degrees)
and with the aim of running MD simulation where the angles do not change
during the simulation
(the off-diagonal elements in fact are set to zero)
Converting then each frame of the
trajectory to a pdb file using gromacs tool "g_trjconv" and
extracting angles from the CRYST1 record of pdb file, I have observed
that my box angles are all varying through out the simulation.
Here my questions are:
1) Why these values of alpha, beta and gamma are changing during the
simulation? I want to run
MD simulations where these values do not change.
2) What might be the correct procedure to keep constant values of these
angles in a triclinic box.
Thank you in advance.
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