[gmx-users] Variation of angles of simulation cell - regd
Mark.Abraham at anu.edu.au
Sun Sep 9 17:47:13 CEST 2012
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.
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