AMBER Archive (2008)

Subject: Re: AMBER: aggregation or cluster detection

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Aug 07 2008 - 10:38:52 CDT

you could also write code to calculate the minimum distance between
different molecules.
amber already has code for something similar and it works well (but
won't for your purpose).
I don't know of any existing code in amber to do this, others that do
aggregation may have codes for you.

On Thu, Aug 7, 2008 at 11:29 AM, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> Hi Fatima,
>
>> I am looking at the aggregation of solute molecules in explicit water.
>> From VMD
>> i can see formation of clusters. I am desperate for a way to detect
>> clustering
>> on a long MD trajectories.
>
> I don't know of a direct way to do this, others may know. However, you might
> be able to short circuit the radial distribution function code in ptraj.
> This lets you specify both a solute and solvent mask. So you could script
> something to write you an input file that calculates an RDF between each
> molecule of interest and the rest of the solvent. You could then follow
> these over time and look for changes that might be indicative of clustering.
> I guess this would work but have never tried it.
>
> Good luck,
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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>
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-- 
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