[gmx-users] Residence time and trjorder

[Carla Jamous]

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

Carla
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110712/5bb7edc3/attachment.html>