[gmx-users] water analysis

[UCT Staff Member - Jackson]

Dear Users
I would like to analyse my trajectory in terms of the probability of
finding water in relation to my peptide.  I have seen this done with
sugars etc where one looks at the 50% probability above bulk density. 
Does anyone have a script that will do this.  I have seen the
griddensity program on the gromacs web site but this seems to be for
analysing water in a membrane pore.

As an alternative, I do have a program that will do what I want but it
is writen for CHARMM.  Is there a script that will change my trajectory
into CHARMM format?

Thanks
Graham
-- 
Professor Graham E. Jackson
Department of Chemistry
University of Cape Town

Tel: (021) 6502531
Fax: (021) 6897499