[gmx-users] Interaction energy calculation in a radius

aloks at mbu.iisc.ernet.in aloks at mbu.iisc.ernet.in
Sat Jan 6 07:16:51 CET 2007

Hi all,
I want to calculate interaction energy between my ligand and residues of
proetins which come within 6A of any atoms of the raidus. I have defined
those residues and ligand as different groups. But how to select water
around 6A radius of the ligand during dynamicsfor the calculation. If I
consider all the water atoms for my calculation, huge contribution by
water molecules, i guess is giving lots of background and so I am getting
+ve values!

Any suggestion would be highly appreciated


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