Re: [modeller_usage] Difference between dynamic_sphere and lennard-jones potential restraints ?

[Modeller Caretaker <modeller-care@salilab.org>]

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.
> 3.Why dynamic_sphere kept as False in this script
> https://salilab.org/modeller/wiki/Mutate%20model ?
Because in that script LJ interactions are used instead. You can 
certainly use dynamic_sphere instead of dynamic_lennard if you like.
	Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org             https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage