Dear Vlad:
The bonds and bond angle constraints in typical MM code are turned off
during energy minimization by default. Without the constraints, bonds
and bond angles can be different from the "ideal" values. During MD, one
usually turns on the constraints to bring the water to TIP3P model.
yong
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of Vlad Cojocaru
Sent: Monday, July 28, 2003 8:42 PM
To: amber
Subject: AMBER: H-O-H angle in TIP3P water model during minimization
Dear Amber users,
trying to get along with Amber TIP3P water in NAMD I noticed
something:
During a simple sander minimization on a system in a waterbox the
H-O-H angle decrease to a value of 98-100 degrees and it is restored to
the value of ~104.5 during equilibration and production runs. Is this
normal and if yes could somebody explain me why?
Best wishes,
Vlad
--
Vlad Cojocaru
Max Planck Institute for Biophysical Chemistry
Department: 060
Am Fassberg 11, 37077 Goettingen, Germany
tel: ++49-551-201.1327
e-mail: Vlad.Cojocaru.mpi-bpc.mpg.de
home tel: ++49-551-9963204
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Received on Tue Jul 29 2003 - 02:53:00 PDT
