[gmx-users] reference distance for Lennard Jones interactions
jalemkul at vt.edu
Sat Oct 20 00:33:40 CEST 2018
On 10/18/18 8:34 AM, kordzadeh at aut.ac.ir wrote:
> I have calculated Lennard Jones interaction between drug and Carbon Nano tube by defining "energygroups" and I got the potential by "gmx energy"
> I have a question, in this figure I have potential versus distance (r), what is the distance? in Lennard Jones equation the distance defines between two atoms, but I don't know what distance will Gromacs consider for interaction while the drug and CNT have a lot of atoms
gmx energy does not write energies as a function of distance, it writes
energies as a function of time. The interaction distances (e.g. whatever
is considered short-range) is set by the cutoffs used in the simulation.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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