ABF, rigid bonds and constraints

From: Ekaterina Sobakinskaja (Ekaterina.Sobakinskaja_at_jku.at)
Date: Fri Jul 06 2018 - 05:23:10 CDT

Dear NAMD developers//and users,

I have a question about using rigid bonds in ABF protocol. I want to get
PMF, using ABF, for a water molecule penetrating a membrane channel. My
colvar is a distance between O atom of a water molecule and CA atom of a
channel residue. As I read in the manual colvars and constraints must be
orthogonal, and this can be satisfied for "pairs of atoms joined by a
constraint bond are part of an /atom group/ which only intervenes
through its center (center of mass or geometric center) in the force
measurement."  So, if I put /rigidbonds water/, it will be satisfied for
water molecules, but what about CA atom? And another question related to
it, what type of PRESSURE control should I use?

thank you very much for the help!

with best regards,


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