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



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
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