[gmx-users] Nonbonded energy of 1-4 interactions

[Justin Lemkul]

On 9/20/18 5:23 AM, Zhonghua Xia wrote:
> Dear all,
>
> I want to get the nonbonded energy (1-4 electrostatic and 1-4 LJ) of solute-solute and solute-solvent, respectively. How can I make it? What’s more, how can I set the scaling-factors of them?

These energies are in LJ-14 and Coul-14 in the .edr file. If you want 
them decomposed for different groups, you need to specify energygrps in 
the .mdp file, re-create a .tpr file with those groups, and post-process 
your trajectory. Note that 1-4 interactions are intramolecular, so there 
is no such thing as a solute-solvent 1-4 energy. The term also has no 
physical meaning as it is completely dependent upon force field 
convention and dihedral terms.

In GROMACS, the 1-4 scaling factors are set with FudgeLJ and FudgeQQ in 
the [defaults] directive of forcefield.itp.

-Justin

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

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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