[gmx-users] nonbond_params directive

Justin Lemkul jalemkul at vt.edu
Sat Jul 28 22:40:41 CEST 2018

On 7/26/18 5:52 PM, Eric Smoll wrote:
> Hello GROMACS users,
> I have a quick question about the nonbond_params directive.
> If I provide gen-pairs=yes and fudgeQQ=0.5 in the defaults directive,
> GROMACS will

That's fudgeLJ, not fudgeQQ, but yes.

> (1) compute VDW parameters for all atomtype-pairs and
> (2) scale all 1-4 interactions specified in the pairs directive by 0.5.
> Note that the parameters for the 1-4 interactions are obtained from (1).


> Will GROMACS still scale all 1-4 interactions by 0.5 if I specify VDW
> parameters for all atomtype-pairs in a nonbond_params directive?

No. [nonbond_params] takes precedence. For any missing pair, and with 
gen-pairs = yes, fudgeLJ is used. It is not used for anything else.



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

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