[gmx-users] accessing pressure components from trajectory file

[Tsjerk Wassenaar]

Hi Aishwary,

Sorry, I appear to be a bit fuzzy. The virial/pressure matrices are written
for any type of pressure coupling. Check Vir-* and Pres-* entries:

 17  Density         18  pV              19  Enthalpy        20  Vir-XX

 21  Vir-XY          22  Vir-XZ          23  Vir-YX          24  Vir-YY

 25  Vir-YZ          26  Vir-ZX          27  Vir-ZY          28  Vir-ZZ

 29  Pres-XX         30  Pres-XY         31  Pres-XZ         32  Pres-YX

 33  Pres-YY         34  Pres-YZ         35  Pres-ZX         36  Pres-ZY

 37  Pres-ZZ                             38  #Surf*SurfTen



Cheers,

Tsjerk

On Tue, Sep 1, 2015 at 8:37 PM, Aishwary Shivgan <
aishwaryshivgan55 at gmail.com> wrote:

> How can I get these pressure values using - rerun option?
> Meaning what changes should be made to mdp file to make new tpr which can
> give me pressure outputs?
>
> On Tue, Sep 1, 2015 at 11:25 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
> > Hi Aishwary,
> >
> > Those components will be in the energy file if you do anisotropic
> pressure
> > coupling. You can't retrieve them from the trajectory, although you can
> > rerun the trajectory to obtain them.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Tue, Sep 1, 2015 at 7:48 PM, Aishwary Shivgan <
> > aishwaryshivgan55 at gmail.com> wrote:
> >
> > > Hi gromacs users,
> > >            I want to get pressure data from trajectory file from each
> > > frame. g_energy gives me only averaged values at each frame but I want
> > Pxy,
> > > Pxx, Pxz and all such pressure components at each frame to calculated
> > > viscosity using green-kubo method.
> > > Is there way to direct way to get them instead of writing code for it?
> > >
> > > Thank you,
> > > Aishwary Shivgan
> > > --
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> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
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-- 
Tsjerk A. Wassenaar, Ph.D.