[gmx-users] water hydration map analysis help

Mark Abraham Mark.Abraham at anu.edu.au
Fri Nov 12 17:44:03 CET 2010

On 13/11/2010 1:21 AM, babu gokul wrote:
> Dear all
> I would like to analysis the hydration site near the proteins the one done by
> the following paper
> "Biophysical Journal Volume 79 December 2000 2966–2974" 
> I would like to do the analysis the trajectory like this.    is there any tool available in gromacs to do this kind of analysis could anyone
> help me in this regard. what tool will be useful to analysis this kind of
> results.

It sounds rather like you're not doing enough of your own work to "earn" 
help. :-) It would take someone several minutes to track down that paper 
from the information you provided, when providing a URL to the paper 
would have been easy and considerate. Then they'd have to spend some 
more time reading parts of it to try and work out what analysis you are 
talking about, in the hope that it's clear which one you are talking 
about. Surely the method description they provided talks enough about 
the geometric primitives that you can provide a quick summary of the 
requirements with a precise and easy pointer to further information once 
you've piqued someone's interest.

This may sound like a lot of work for you, but see 

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