Hi,
The cpptraj command ‘volume’ will calculate the volume of any unit cell
shape.
-Dan
On Wed, Aug 4, 2021 at 1:52 AM Umesh Roy <umesh24crp.gmail.com> wrote:
> Thank you very much for your reply. Yes, the box size may change during
> simulation. Maybe I should have placed my query in a better way. More
> precisely, I would like to know how the box dimension (Box X, Box Y, and
> Box z) is related to the volume of the truncated octahedron. Since the
> values of the box dimension are saved at a certain interval (at which we
> save our trajectories) during MD run in the coordinate file. How can I
> relate the volume of the truncated octahedron to the box dimension at a
> particular step?
>
> Thank you.
>
>
> With best regards,
>
>
> Umesh
>
>
> On Wed, Aug 4, 2021 at 6:38 AM David A Case <dacase.chem.rutgers.edu>
> wrote:
>
> > On Wed, Aug 04, 2021, Umesh Roy wrote:
> >
> > >> solvateOct protein TIP3PBOX 10
> > >
> > >%FLAG BOX_DIMENSIONS
> > >%FORMAT(5E16.8)
> > > 1.09471219E+02 *6.31036082E+01 6.31036082E+01 6.31036082E+01*
> > >%FLAG RADIUS_SET
> >
> > Two points here:
> >
> > First: since the box size (often) changes during a simulation, it should
> > never have been put into the prmtop file -- the prmtop file is for things
> > that don't change. So, the information in the prmtop file is ignored:
> box
> > information is always taken from the coordinate file. (The information
> is
> > still there for backwards compatibility with *very* old files.)
> >
> > (Second: however, the 109.47 value above did originally indicate that
> this
> > was a truncated octahedron, and not a cubic box.)
> >
> > >* Box X = 63.104 Box Y = 63.104 Box Z = 63.104*
> > > Alpha = 109.471 Beta = 109.471 Gamma = 109.471
> >
> > Above is the box information taken from the input coordinate file.
> >
> > >This means that box information saved in the topology file is used for
> the
> > >subsequent/production run.
> >
> > This is not correct. As noted above, any box information in the prmtop
> > file
> > is ignored.
> >
> > ...hope this helps....dac
> >
> >
> >
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Received on Wed Aug 04 2021 - 13:30:03 PDT
