[AMBER] Apply Lennar-Jones potential between small molecules

From: Ming Tang <m21.tang.qut.edu.au>
Date: Wed, 24 Feb 2021 22:51:46 +0000

Dear list,

I have a system of protein with lot so small molecules solvated in a water box. I want to apply force/potential between the centre of mass a group of atoms in different small molecules to prevent them from aggregation. I only know AMBER can define non-bounded interactions between two atoms using LJEDIT in *.frcmod. Is there a way to define a virtual particle as the centre of mass of a certain group of atoms? Does anybody have any advice for me?



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Received on Wed Feb 24 2021 - 15:00:02 PST
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