On Tue, Feb 16, 2010, Yubo Fan wrote:
>
> I'm trying to do some simulations with PBC for bonding interactions.
> For example, graphite. The carbon atoms connecting from one end to the
> other should have covalent bonds. But the Amber seems not to compute
> the bond energy using PBC. The calculations failed with exceptionally
> long bond lengths. I'm trying to modify the pmemd code by passing
> pbc_box information into bonds.fpp, angles.fpp and dihedrals.fpp but
> did not figure out how. Any advise? Thanks in advance.
Amber is not coded for periodic simulations in which there are covalent bonds
across unit cells.
....dac
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Received on Tue Feb 16 2010 - 05:00:02 PST
