Re: Colvar: minimal distance between 2 groups of atoms

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Nov 17 2014 - 10:07:38 CST

Indeed, but the larger the negative exponent, the more this average is
skewed towards the smallest distances in the set, making it a possible
approximation to the minimal distance. If that is not steep enough, the
power function can be replaced with an exponential, but it's still a form
of average. By the way, that would be really easy to implement if there is
demand for it.

Jerome

On 17 November 2014 16:57, Vlad Cojocaru <vlad.cojocaru_at_mpi-muenster.mpg.de>
wrote:

> But this looks more like an average distance than a minimum distance,
> isn't it ?
>
>
>
> On 11/17/2014 03:49 PM, Giacomo Fiorin wrote:
>
> Can you try distanceInv choosing the exponent that gives you the best
> behavior?
> On Nov 17, 2014 8:42 AM, "Vlad Cojocaru" <
> vlad.cojocaru_at_mpi-muenster.mpg.de> wrote:
>
>> Dear NAMD users,
>>
>> Could you please let me know if it is currently possible to define the
>> minimal distance between 2 groups of atoms as a colvar component within the
>> colvar module ?
>>
>> Thanks
>>
>> Best wishes
>> Vlad
>>
>> --
>> Dr. Vlad Cojocaru
>> Computational Structural Biology Laboratory
>> Department of Cell and Developmental Biology
>> Max Planck Institute for Molecular Biomedicine
>> Röntgenstrasse 20, 48149 Münster, Germany
>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>> http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>>
>>
> --
> Dr. Vlad Cojocaru
> Computational Structural Biology Laboratory
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.dehttp://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>
>

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