AMBER Archive (2008)

Subject: AMBER: aggregation or cluster detection

From: fatima.chami_at_durham.ac.uk
Date: Thu Aug 07 2008 - 08:41:24 CDT

Dear Amber's users,

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 have downloaded th MMSTB tool set but this does only clustering analysis on
conformations and what I am looking is nucleation rate or in an other word
formation of clusters.

If any one has come across this matter..I will be glad to know

I am not sure if the VMD package can extract such information from an MD
trajectories

best wishes
Fatima

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