Re: [AMBER] SolvateOct box volume and cubic box information

From: Umesh Roy <>
Date: Thu, 5 Aug 2021 10:27:15 +0530

Thank you for your reply.

On Wed, 4 Aug 2021, 17:40 David A Case, <> wrote:

> On Wed, Aug 04, 2021, Umesh Roy 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?
> One presentation of the formula is here:
> The final line of a (formatted) coordinate file gives
> a,b,c,alpha,beta,gamma.
> For a truncated octahedron, there is a single cell length and an single
> angle, so you could simplify the formula some.
> If you are doing constant pressure simulations (so that the unit cell
> volume
> is changing), the volume is printed out along with the energies in the
> mdout
> file.
> ....dac
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Wed Aug 04 2021 - 22:00:02 PDT
Custom Search