[gmx-users] On the box type

[Mark Abraham]

On Sun, Jul 7, 2013 at 4:15 PM, akcyrus <akcyrus at gmail.com> wrote:
> Dear all and Tsjerk Wassenar,
> I could not grasp how a rectangular box will be a problem. Lets assume a I
> have a cylinder of radius r (nm) and height h (nm) with h>r. I place the
> cylinder aligned along z-axis and then in a rectangular box with dimension
> 2r+2.0 nm, 2r+2.0 nm and 2h+2.0 nm. My understanding is that the problem
> could be when during simulation, the cylinder gets aligned parallel to XY
> plane and the box vectors are shorter along X and Y,isn't that right?

Yes. If that can happen, then your simulation will become junk when it does.

> Also
> during the simulation, with isotropic pressure coupling the box tend to be
> cubic and this would also cause problems. Correct me if I am wrong or don't
> understand it right.

Anisotropic coupling is available. But I don't think that is an issue
in choosing whether a rectangular box is plausible.

Mark