[gmx-users] Turning off charges of a particular atom type

Justin Lemkul jalemkul at vt.edu
Tue Sep 25 23:56:21 CEST 2012

On 9/25/12 5:54 PM, Andrew DeYoung wrote:
> Hi,
> If you have time, I have one more question.  Suppose that I have some atom
> type named XX.  Normally XX has a partial charge, but for a test simulation,
> I would like to turn off the charges of all of the XX atoms.  This way, I
> will hopefully be able to disentangle the relative effects of Coulomb
> interactions (i.e., charges) and van der Waals/Lennard-Jones interactions in
> my system.
> Is it true that to turn off the charges of the XX atoms, I can simply set
> the charge parameter in my nonbonded topology (e.g., ffnonbonded.itp) to 0?
> Or is there a better way to do this?

Charges in ffnonbonded.itp are not used.  You would have to zero out the charges 
in the topology (.top or .itp).



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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