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

From: Ming Tang <>
Date: Mon, 15 Mar 2021 23:28:21 +0000

Hi Carlos,

should rk2 be negative when applying repulsive for between two groups closer than r2? When I set it to 50, the two groups are close but the restrain in output file is 0.


-----Original Message-----
From: Carlos Simmerling <>
Sent: Friday, 26 February 2021 3:02 AM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Apply Lennar-Jones potential between small molecules

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:;!!NVzLfOphnbDXSw!TI_PpsbMCL8Whg8o7-3O7qAwmtKzGL2a_c4Q-vx_db-A5zB7SGvlObCAU4veBB_2eqzW$

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

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
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