[gmx-users] Variations of angles in a triclinic box
tsjerkw at gmail.com
Wed Apr 22 16:19:27 CEST 2015
You scale the axes separately. so you may stretch one component of a
vector, and/or compress one, thus changing the angle.
On Wed, Apr 22, 2015 at 4:15 PM, Antonio Pizzirusso <
antonio.pizzirusso80 at gmail.com> wrote:
> 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.
> Best regards,
> Gromacs Users mailing list
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Tsjerk A. Wassenaar, Ph.D.
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