[gmx-users] Lennrd-Jones potential in Gromos force field

[Justin Lemkul]

On 6/13/18 7:16 PM, kordzadeh at aut.ac.ir wrote:
> ​Hi Dr.Abraham
> Thank you very much for your answer, I couldn't recognize my problem that , what does LJ-SR indicate in gmx energy module, vdw, polar-polar, nonpolar-nonpolar or other interactions?
> Thanks in advance for your answer and your help

LJ-SR gives you the energy from the Lennard-Jones equation for all atom 
pairs that are within the short-range cutoff. gmx energy doesn't attempt 
to be smart about the chemical nature of the atoms/molecules. 
Definitions of "polar" and "nonpolar" are largely from electrostatics, 
anyway, which has no bearing on LJ energies. All atoms (except sometimes 
H) have LJ terms and will be included in this calculation.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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