From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Thu May 24 2012 - 02:13:29 CDT
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.mpg.de
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