From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Thu May 24 2012 - 09:47:45 CDT
Of course you are right ... One can use a 2 component colvar to do the
job ... One can use "distance" and "angle" or "hbond" and "angle"
But I started with the idea that "hbond" would allow the use of a
single-component colvar for a hydrogen bond ... Of course, I understood
from the manual and from my trials that this is not the case..
On 05/24/2012 03:58 PM, Giacomo Fiorin wrote:
> 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
> <mailto:vlad.cojocaru_at_mpi-muenster.mpg.de>> 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
> 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 <tel:%2B49-251-70365-324>; Fax:
> +49-251-70365-399 <tel:%2B49-251-70365-399>
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
-- 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.mpg.de -- 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.mpg.de
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