[gmx-users] Variations of angles in a triclinic box
antonio.pizzirusso80 at gmail.com
Thu Apr 23 08:53:57 CEST 2015
Thank you very much for your reply and valuable
Is possible to simulate using appropriate values in pressure
parameters a triclinic box without varying
2015-04-22 16:19 GMT+02:00 Tsjerk Wassenaar <tsjerkw at gmail.com>:
> Hi Antonio,
> 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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