Re: hbonds colvar component

From: Giacomo Fiorin (
Date: Thu May 24 2012 - 08:58:04 CDT

Hi Vlad, why don't you add instead an "angle" component to the variable
containing "hbond"? You keep the "hbond" component, which goes from 0 to
1, and define "componentCoeff" as 0.5. Then you also add an angle with
"componentCoeff" equal to 0.5/180. When the angle is equal to 180° and the
distance is within the cutoff, you get an improved hbond variable that
takes the angle into account. If you think that the variable is not
sensitive enough to the angle, you may play with componentExp to make the
angle term vary more steeply.

None of the above requires editing the source code, so you can optimize it
as much as you want for your specific problem.


On Thu, May 24, 2012 at 3:13 AM, Vlad Cojocaru <> wrote:

> Dear all,
> I am trying to use the "hbond" colvar to fix a model by imposing certain
> hydrogen bonds to form (we know they should be there but the model has
> quite a bad geometry for these interactions). Unfortunatel, regular MD doe
> not fix them in reasonable time. Furthermore, I have the feeling that the
> simulation shows strange dynamics because it is not able to fix these
> interactions.
> In the colvar simulations however (colvars defined for each hydrogne bond,
> one component "hbonds" for each colvar, harmonic restraints applied with a
> force ct of 100), I never get a nice hbond geometry (distance
> donor-acceptor < 3.0 and donor-H-acceptor angle < 30 deg) ... I think the
> reason for this is because the "hbond" colvar component does not consider
> the angle but rather takes only the distance as a criterion for hydrogen
> bond formation.
> So, it seems at the moment that this colvar component is not very useful
> for defining hydrogen bonds ...
> First of all, if my reasoning is wrong, please let me know.
> Second, is there a plan to have a colvar component "hbond" that really
> takes the angle into consideration as well ? Or shall we just use a
> combination of angle and distance colvars to define hbonds.
> Best wishes
> Vlad
> --
> Dr. Vlad Cojocaru
> Max Planck Institute for Molecular Biomedicine
> Department of Cell and Developmental Biology
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.** <>

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