Re: ABF, rigid bonds and constraints

From: Ekaterina Sobakinskaja (
Date: Fri Jul 06 2018 - 10:06:21 CDT

Dear Jerome,

thank you for the help!


On 2018-07-06 13:03, Jérôme Hénin wrote:
> 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
> < <>>
> 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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