From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Mon Nov 17 2014 - 10:14:58 CST
Below is how PLUMED implements the minimal distance and this looks more
in the direction you mention ..... The problem with PLUMED is that in
apparently does not allow NPT simulations with NAMD ... I also don't
know how PMF calculations with PLUMED versus COLVAR scale with NAMD
http://plumed.github.io/doc-v2.0/user-doc/html/mindist.html
Best
Vlad
On 11/17/2014 05:07 PM, Jérôme Hénin wrote:
> 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
> <mailto: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
>> <mailto: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 <tel:%2B49-251-70365-324>; Fax:
>> +49-251-70365-399 <tel:%2B49-251-70365-399>
>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>> <http://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.de <http://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.de http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
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