AMBER Archive (2008)

Subject: RE: AMBER: aggregation or cluster detection

From: Ross Walker (
Date: Thu Aug 07 2008 - 10:29:28 CDT

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,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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