[gmx-users] Variations of angles in a triclinic box

[Tsjerk Wassenaar]

Hi Antonio,

You scale the axes separately. so you may stretch one component of a
vector, and/or compress one, thus changing the angle.

Cheers,

Tsjerk

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
> always
> 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,
>
> Antonio
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-- 
Tsjerk A. Wassenaar, Ph.D.