Re: [AMBER] Apply Lennar-Jones potential between small molecules

From: Carlos Simmerling <>
Date: Thu, 25 Feb 2021 12:01:46 -0500

you might try using a distance restraint that has rk2=0, this will give no
penalty for distances longer than r2 and a harmonic penalty below r2. You
can define groups of atoms for COM distance restraints.

check the manual for details (use the nmropt=1 option), and then create a
restraint that looks something like this (making sure to edit the atom
numbers, distances and force constants). igr1 and igr2 list the atoms in
each COM group. r1/r2/r3/r4 define the distance points where the function
changes. rk2 and rk3 are the force constants. The function is described in
this tutorial:

  r1=1.0, r2=10.0, r3=900.0, r4=1000.0, rk2=10., rk3=0.0,

On Wed, Feb 24, 2021 at 5:52 PM Ming Tang <> wrote:

> 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?
> Thanks,
> Ming
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Thu Feb 25 2021 - 09:30:02 PST
Custom Search