**From:** Ajasja Ljubetič (*ajasja.ljubetic_at_gmail.com*)

**Date:** Mon Nov 17 2014 - 11:30:45 CST

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Hmm, but what is the width of distributions in each separate component?

If you have the distances between atoms of the groups in the range of

(2.5,40) then n=10^7 will get you to 2.563 A

(and you will probably need the exponential weighting).

If on the other hand you have distances on the (40, 42.5) the n=10^5 will

get you to 40.004 A.

Best regards,

Ajasja

Disclaimer: These are only back of the envelope calculations done as a

break from writing my PhD:) I have no previous experience with distanceInv.

On 17 November 2014 17:49, Vlad Cojocaru <vlad.cojocaru_at_mpi-muenster.mpg.de>

wrote:

*> 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.
*

*>
*

*> [image: 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
*

*> [image: Inline images 2]
*

*>
*

*> Good luck & best regards,
*

*> Ajasja
*

*>
*

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

*> 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> 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
*

*>>>
*

*>>>
*

*>>
*

*>> --
*

*>> 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
*

*>>
*

*>>
*

*>
*

*> --
*

*> 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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