[gmx-users] Residence time and trjorder

Carla Jamous carlajamous at gmail.com
Tue Jul 12 14:04:31 CEST 2011

Dear gmx-users,

I used trjorder in order to study the water molecules that are closer than 5
A from my protein.

trjorder -s structure.tpr -f traj.xtc -n prot_water.ndx -o ordered.pdb
-nshell nshell_.xvg -r 0.5 -b 0 -e 5000

But now I need to analyse the residence time of a water molecule, I mean the
number of times a single water molecule stays in a radius of 5 A of the
protein and divide this number by the total number of conformations, in
order to have a pourcentage value.

Please is there any gromacs tool able to do this calculation or else does
anyone have an idea of how to do that?

Thank you

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