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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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