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

**Date:** Tue Nov 18 2014 - 03:40:53 CST

**Next message:**Douglas Houston: "Re: About NAMD"**Previous message:**Jim Phillips: "NAMD 2.10b2 released"**In reply to:**Ajasja Ljubetič: "Re: Colvar: minimal distance between 2 groups of atoms"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

The ranges are between 2.5 and 45 Angstr ... what we can do (if colvars

allows that) also is to update the selection and consider only those

atoms of component 1 within 10 Angstr of component 2 ... then we'd have

ranges between 2.5 and 10 Angstr at the beginning of PMF and between 6

and 10 at the end of the PMF ...

Vlad

On 11/17/2014 06:30 PM, Ajasja Ljubetič wrote:

*> 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
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*> 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
*

*> <mailto: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.
*

*>>
*

*>> 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 <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

**Next message:**Douglas Houston: "Re: About NAMD"**Previous message:**Jim Phillips: "NAMD 2.10b2 released"**In reply to:**Ajasja Ljubetič: "Re: Colvar: minimal distance between 2 groups of atoms"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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