**From:** Vlad Cojocaru (*vlad.cojocaru_at_mpi-muenster.mpg.de*)

**Date:** Mon Nov 17 2014 - 10:49:57 CST

**Next message:**Ajasja Ljubetič: "Re: Colvar: minimal distance between 2 groups of atoms"**Previous message:**Ajasja Ljubetič: "Re: Colvar: minimal distance between 2 groups of atoms"**In reply to:**Ajasja Ljubetič: "Re: Colvar: minimal distance between 2 groups of atoms"**Next in thread:**Ajasja Ljubetič: "Re: Colvar: minimal distance between 2 groups of atoms"**Reply:**Ajasja Ljubetič: "Re: Colvar: minimal distance between 2 groups of atoms"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Thanks a lot ...

Our distances are between a few Angstr (e.g. 2.5) and a few tens of

Angstr (e.g 40) between a 2 component system. For the dissociation PMF

calculation we'd need a resolution of 0.05 Angstr (center of the PMF

window would change by 0.05 Angstr minimal distance) ...

Basically. we are doing the types of simulations described by Bouvier

and Lavery (http://pubs.acs.org/doi/abs/10.1021/ja901761a) and we are

looking for an alternative to the original code (a mixture of tcl forces

and C code implemented for NAMD) because we encountered some

RATTLE-related problems when using it with our systems as well

performance limitations (especially scaling) ...

Best

Vlad

On 11/17/2014 05:28 PM, Ajasja Ljubetič wrote:

*> Here is a quick plot of inverse distance versus n for a uniform
*

*> distribution on the interval (1,2). As you can see, with increasing n
*

*> the value of the distance approximates the minimum distance.
*

*>
*

*> Inline images 1
*

*>
*

*> If your distances are large, you may have to set n to large values.
*

*> So barring any precision issues this approach should work.
*

*>
*

*> For example for values in the range of (100,101) with n=10000
*

*> Inline images 2
*

*>
*

*> Good luck & best regards,
*

*> Ajasja
*

*>
*

*> On 17 November 2014 17:14, Vlad Cojocaru
*

*> <vlad.cojocaru_at_mpi-muenster.mpg.de
*

*> <mailto:vlad.cojocaru_at_mpi-muenster.mpg.de>> wrote:
*

*>
*

*> 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 <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 <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://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru

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