AMBER Archive (2008)

Subject: Re: AMBER: How to manually adjust periodic boundary conditions (PBC)

From: David A. Case (
Date: Thu Nov 20 2008 - 14:52:57 CST

On Wed, Nov 19, 2008, Chin, Keith B wrote:
> How do I manually set periodic boundary conditions to hexagonal crystal
> lattice with alpha = 90, beta = 90, gamma = 120 (NOT box with alpha = 90,
> beta = 90, gamma = 90) to run MD in sander? I used the setbox command to
> set initial PBC close to actual lattice dimensions prior to changing it in
> last line of *crd (coordinate) file.

Sounds correct; generally, the coordinates override what is in the prmtop
file, but to be safe, you should modify the prmtop file as well. Simulating
non-orthogonal boxes is not well-documented, so you have to be willing to
experiment and to study the relevant code.


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