From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu May 24 2012 - 10:12:51 CDT
Most of the times just the contact between the donor and the acceptor works
fine. Adding the angle term would improve the H-bond's definition, but
also involve the hydrogen at all times, which due to its light mass could
respond with higher instability to strong restraints.
There is always a trade-off in choosing how to set up a simulation.
One way of not having to deal with trade-off and compromise may be to treat
the H-bond for what it actually is, i.e. a quantum phenomenon?
Giacomo
On Thu, May 24, 2012 at 10:47 AM, Vlad Cojocaru <
vlad.cojocaru_at_mpi-muenster.mpg.de> wrote:
>
> Hi Giacomo,
>
> 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..
>
> Best wishes
> Vlad
>
>
> 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.
>
> Bests
> Giacomo
>
> On Thu, May 24, 2012 at 3:13 AM, Vlad Cojocaru <
> 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
>> 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
>>
>>
>>
>
> --
> 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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