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

**Date:** Mon Nov 17 2014 - 12:12:42 CST

**Next message:**Jérôme Hénin: "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:**Jérôme Hénin: "Re: Colvar: minimal distance between 2 groups of atoms"**Reply:**Jérôme Hénin: "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 November 17, 2014 6:30:45 PM CET, "Ajasja Ljubetič" <ajasja.ljubetic_at_gmail.com> 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
*

*>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
*

*>>
*

*>>
*

-- Sent from my Android device with K-9 Mail. Please excuse my brevity.

**Next message:**Jérôme Hénin: "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:**Jérôme Hénin: "Re: Colvar: minimal distance between 2 groups of atoms"**Reply:**Jérôme Hénin: "Re: Colvar: minimal distance between 2 groups of atoms"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Thu Dec 31 2015 - 23:21:23 CST
*