[gmx-users] Nonbonded energy of 1-4 interactions
jalemkul at vt.edu
Fri Sep 21 14:41:00 CEST 2018
On 9/21/18 8:25 AM, Zhonghua Xia wrote:
> Hi Justin,
> Thank you so much for your answer!
> So, if I want to calculate the nonbonded energy of solute-solute and solute-solvent, I should set the parameter as below:
> energygrps = MOL MOL MOL SOL
No, just energygrps = MOL SOL
mdrun builds the matrix from the listed groups. Again, be aware that for
most force fields, this quantity has no physical meaning.
> And If I want to customise FudgeLJ and FudgeQQ, is it feasible to directly modify their values in the forcefield.itp file?
You can modify it, but then you break the force field convention because
you invalidate all the dihedral parameters, which require a given 1-4
scaling to be balanced.
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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