Re: restrain lateral movement during ABF

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu May 17 2018 - 08:03:50 CDT

DistanceXY is just a name, it can function with any axis you choose (see
the axis keyword).
http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:cvc_distanceXY

If a fixed axis does not work because of overall protein rotation, you can
make that a moving axis tied to the protein frame of reference.
http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvar_atom_groups_ref_frame

Best,
Jerome

On 16 May 2018 at 23:34, Olya Kravchenko <ovkrav_at_gmail.com> wrote:

> Hi all,
>
> I am trying to restrain lateral movement of the ion when it is just
> outside the entrance of the channel during ABF calculations. My reaction
> coordinate is the distance between the center of mass of the spherical
> protein and the ion; it does not coincide with z axis, so I can't use
> distanceXY. The protein is spherical, and the outer surface is convex. Is
> there a colvar that I can use in such a case to keep the ion in place?
>
> If I were to make a tclBC script that would return the ion inside a sphere
> of a small radius located just outside the entrance of the channel, how
> would that affect ABF outcome for that window? Will such script interfere
> with a similar script that I use to push out salt ions from entering the
> channel?
>
> Thank you,
>
> Olga
>

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