[gmx-users] Nonbonded energy of 1-4 interactions
jalemkul at vt.edu
Thu Sep 20 16:39:03 CEST 2018
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 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
More information about the gromacs.org_gmx-users