[gmx-users] Analysis of solvent dynamics

James Starlight jmsstarlight at gmail.com
Tue Dec 11 10:58:32 CET 2012

Dear Gromacs Users!

I want to study dynamics of solvent burried into the protein interiour
during simulation (to check solvent accessible  area of different
amino acid of my protein). Eg while simulating of Green Fluorescent
protein I'd like to check how much water burried into the beta-can
interiour of that protein ( which can effect chromophore of that
protein for instance).

What Gromacs utilites can be suitable for such analysis?
I've tried to make such study with the g_rdf but I'm not quite sure
about suitability of that tool for my task ( e.g what is the ref_group
as well as first group about which program ask me when i tried g_rdf
-f wild_Chimera_15ns.xtc -s minim.tpr -n index.ndx -cut 0.4 ) ?

Thanks for help


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