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 Tue Aug 03 2021 - 23:00:03 PDT
