From: Stojanoski, Vlatko (stojanos_at_bcm.edu)
Date: Sat Oct 17 2015 - 14:05:29 CDT
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,
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