From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Wed Mar 15 2006 - 19:34:22 CST
Hi,
I am developing some dihedral parameters for a molecule with a cage
structure. If the cage atoms are typed identically, then there are
multiple dihedral energy minima without a periodicity (e.g., +/- a
certain angle). I believe AMBER permits multiple instances of the same
parameter to be given, but NAMD is issuing messages
Warning: IDENTICAL PERIODICITY! REPLACING OLD VALUES BY:
as it reads the parameter file, implying that it is replacing each older
instance of a parameter by the latest one, rather than adding a new
minimum to the potential function. How does NAMD handle this situation,
and how can I specify multiple non-periodic minima in the potential?
Thanks,
Chris
Christopher H. Chang, Ph.D.
Research Associate
National Renewable Energy Laboratory
1617 Cole Blvd., Mail Stop 1608
Golden, CO 80401
Phone (303) 275-3751
Fax (303) 275-4007
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