Dear all,

I am a bit confused about [ dihedral constraints ].

I was planning to contraint a dihedral in a "flat-bottom" way, so that
e.g. angles between 120 and 240 deg are sampled, but above 240 and below
140 are basically "not allowed". In other words, I just want a harmonic
potential, where the point of zero-potential is stretched from a point
Theta_0 to a range of Theta_0 +- delta_Theta.

Dihedral restraints seemed to be what I need, at first glance, but I am
confused about the resulting potential obtained from equation 12 in the
manual:
http://manual.gromacs.org/current/reference-manual/functions/restraints.html#dihedralrestraint

The conditions
- |Theta'| > delta_Theta
- |Theta'| <= delta_Theta
and the "(Theta' - delta_Theta)" in the first condition of eq. 12 will do
it in an asymmetric way, with different behaviour at Theta' = +
delta_Theta or Theta' = - delta_Theta.

Therefore, is equation 12 just written in a strange way and it creates a
symmetric flat-bottomed potential or will it really result in such an
asymmetry?

Thanks already for your help.

Best wishes,
Jacek

________________________________________________
Dr. Jacek Kozuch

Freie Universit├Ąt Berlin
Fachbereich Physik
Arnimallee 14
Raum 1.1.35
14 195 Berlin
________________________________________________


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