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
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