How to Selectively Scale Interactions

From: Matthew Guberman-Pfeffer (
Date: Thu Oct 22 2020 - 23:30:47 CDT

Dear NAMD Community,

I would like to assess the relative stability of two multimeric protein
assemblies where one is missing subunits found in the other. Is there a way
to selectively scale-down the non-bonded inter- (but not intra-) protein
interactions to use the scaling factor as the variable for
thermodynamic integration?

More generally, if there are better approaches for assessing relative
protein assembly stability, I'd greatly appreciate the advice.


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