Re: ABF, rigid bonds and constraints

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Jul 06 2018 - 06:03:00 CDT

Dear Ekaterina,

The simplest option is to consider the complete water molecule on one side,
and the CA-HA pair on the other.

There are no particular restrictions on the barostat.

best,
Jerome

On Fri, 6 Jul 2018 at 12:24, Ekaterina Sobakinskaja <
Ekaterina.Sobakinskaja_at_jku.at> wrote:

> 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,
>
> Ekaterina
>

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