Re: Performing MD simulations with protein and halide ions (iodide, bromide, chloride)

From: Branko (
Date: Sat Oct 17 2015 - 14:35:37 CDT


CHARMM force field support majority of halide ions (for example Clminus
is commonly used as counter ion to 'neutralize' positively charged
protein). So, you should look in parameter files available from
Also see:
Alternatively, you could use VegaZZ as GUI
In this software preparation of NAMD input (including addition of ions)
is really user-friendly


On 10/17/2015 9:05 PM, Stojanoski, Vlatko wrote:
> Dear NAMD users,
> I'm relatively new to the MD simulations and previously I have managed
> to perform MD simulations of proteins in a solvent box with the NVT
> ensemble using the NAMD Graphical interface in VMD.
> However, now I'm trying to perform simulations of proteins that
> interact with halide ions (iodide, bromide, and chloride in
> particular) and I'm not sure how to go about it. I know that I need to
> create parameters for the ions but not sure how. Any help or pointing
> in the right direction are greatly appreciated. Thank you beforehand!
> All the best,
> Vlatko

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