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

[Justin Lemkul]

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

-- 
==================================================

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================