AMBER Archive (2004)

Subject: AMBER: intramolecular energies

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Mon Sep 27 2004 - 16:17:11 CDT

Dear all,

I'm looking at calculating intramolecular energies for a periodic system
(organic fluid) with PME. Is there a convenient way of doing this with
the current sander code? If I need to change sander code to make this
happen, would it be a reasonable idea to play with the nonbond-list to
include all atoms in the same molecule? I'm totally unfamiliar with PME
code and nonbond list generation/management. I'd greatly appreciate it
if anyone can give me a few pointers where I should start looking.

Thanks.

Regards,

Guanglei
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