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.
...dac
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Received on Fri Dec 05 2008 - 16:11:31 PST
