Hello,
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.
Yubo Fan
Chemistry Department
Texas A & M University
Tel: (979) 845-5237
Email: yubofan.mail.chem.tamu.edu
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Received on Tue Feb 16 2010 - 01:00:03 PST
