VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Sep 04 2008 - 07:51:51 CDT

Hi Regina,
there are two ways that angle terms and dihedral terms can end up in
your simulations: they can either be explicitly defined in the topology
file by an
ANGLE #1 #2 #4 or DIHE #1 #2 #3 #4 line, or, if a segment is build with
AUTO ANGL DIHE set, all angles and dihedrals consistent with the defined
bonds for that segment are generated (this is, for example, what is done
for proteins when you use charmm topology files). If a dihedral angle is
not specified using one of these two methods then it won't show up in
the psf, and won'thave a potential associated with it in namd.

Peter

politr_at_huji.ac.il wrote:
> Dear VMD users and developers,
> Does anyone knows what means definition of DIHE in topology file? I
> know that it is definition of dihedral angles but does NAMD use this
> definition in some way? If this angles are defined in topology file
> can it cause to rigidity of defined angles during the simulation.
> Regina