Re: [modeller_usage] Difference between dynamic_sphere and lennard-jones potential restraints ?
To: Mahesh Velusamy <>,
Subject: Re: [modeller_usage] Difference between dynamic_sphere and lennard-jones potential restraints ?
From: Modeller Caretaker <>
Date: Mon, 12 Dec 2016 20:51:05 -0800
On 12/12/16 5:09 PM, Mahesh Velusamy wrote:
1.what is the difference between these two restraints in terms (when to
use) usage ?
Soft sphere penalizes interpenetration of two atoms's vdw spheres using
a simple harmonic function. Lennard Jones uses the full 6-12 potential.
Soft sphere is cheaper since you can use a shorter nonbond cutoff
distance, but less accurate because you miss the long range attractive
component. You can use whichever one you want - it doesn't make a huge
amount of difference.