# Re: Colvar: minimal distance between 2 groups of atoms

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Nov 17 2014 - 11:30:45 CST

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.

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