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
--
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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