[gmx-users] gmx trjorder

[Pandya, Akash]

Hi,

I would like to calculate the number of ligand molecules within 0.5 nm of a particular amino acid in my protein. I came across the gmx trjorder command (as shown below).


gmx trjorder -f Traj.gro -s Traj.tpr -n ProteinLIG.ndx -nshell nshell1.xvg -b 20000 -e 40000 -na 10 -r 0.5


I have 10 atoms in my ligand. I wanted to ask how accurate is this command in trying to calculate what I want?


Akash