bunch of water molecules

From: sathish kumar gurupatham (sathishguru1_at_gmail.com)
Date: Thu Aug 09 2007 - 13:39:51 CDT

hi all,
i am simulating a bunch of water molecules at 310k.( to learn namd)
I am getting a lot of fluctuations during minimisation for angle and bond
potentials
but at the end they reduce to zero (suddenly).
and during equilibration they remain zero through out.
is right?
does it mean the molecules do not have angle and bond potentials?
if yes, how?...am i wrong in simulation?
please help me learn the basics.
thanks in advance.
sathish.

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