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

[Antonio Pizzirusso]

Dear Tsjerk,

Thank you very much for your reply and valuable
suggestions,

Is possible to simulate using appropriate values in pressure
parameters a triclinic box without varying

the angles?



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.
>
> 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.
>
>