[gmx-users] Analyze neighbors of a residue within a cutoff distance during simulation

[Tushar Ranjan Moharana]

Hi Everyone,
I have simulated a protein in 40 % methanol. Now I want to analyze the
average distance between any amino acid and all the methanol molecule which
comes to close to (less than 0.4 nm) that amino acid during the simulation.
I tried many GROMACS analysis tool for this but I couldn't succeed. Can
anybody kindly suggest me which analysis tool will be useful for me.

Thanks a lot in advance.


"A society with free knowledge is better than a society with free food"

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB