[gmx-users] channel size calculation between active site lid

[raja]

Hi all,
I followed center of mass (COM) between lids region (two loops covering
the entrance of active site) during simulation to see its action of
opening and closing. Normally COM varies for all simulation of my
protein (Wild and its mutant variant) is between 17A to 20A. Now I want
to find out the average opening size (Pore or channel size) during
simulation through which the substrate believed to reach the active
site. How to do it either within or outside of gromacs?

With thanks!
B.Nataraj
-- 
  raja
  raja_28 at fastmail.us

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