[gmx-users] Analysis of buried water dynamics

James Starlight jmsstarlight at gmail.com
Wed Jun 20 10:49:22 CEST 2012

Dear Gromacs users!

I'm simulatting membrane receptor in the explicit membrane surrounded by
water. Durring this MD run I've noticed that individual waters move into
the receptor interiour from the surroundings leaflets ( In my case mainly
from upper leaflet). How I could examine dynamics of such burried waters (
e.g calculate wich exactly water mollecule moves into protein interiour and
on what timescale this dynamics is observed ) as well as obtain time-life
of such burried water into the receptor interiour?  Also I wounder to know
if it possible to obtain information about dynamics non-covalent
interactions of such water ( define interaction residues with such water )

Thanks for help,

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