Force Field Parametrization

From: Ramon Mendoza Uriarte (
Date: Sun Dec 27 2020 - 19:08:44 CST

Hello NAMD community,

I want to simulate a protein, ion, water, and lipids system at a more attractive nonbonded interactions between segments of the protein and the ions. Does anyone have any insight to this? I am using the CHARMM force filed parameters.

Would NAMD's nonbondedScaling be helpful for this? Or, would I need to modify the entirety of the protein parameter file? If I modify the ion and amino acids parameters that I want to be more attractive (Aside: I'm unsure of how I would specifically target segments of the protein to be more attractive to the ions, thus the reasoning to my approach) I think I would then have to change all parameters so that the overall interactions stay "physical" except for those that I want to be more attractive.

Any thoughts would be very much appreciated!

Thank you,

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