How to Selectively Scale Interactions

From: Matthew Guberman-Pfeffer (matthew.guberman-pfeffer_at_yale.edu)
Date: Thu Oct 22 2020 - 23:30:47 CDT

• Next message: zeynab hosseini: "Re: well-tempered metadynamics deforms the water box and the system becomes unstable.."
• Previous message: Giacomo Fiorin: "Re: well-tempered metadynamics deforms the water box and the system becomes unstable.."
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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.

Best,
Matthew

• Next message: zeynab hosseini: "Re: well-tempered metadynamics deforms the water box and the system becomes unstable.."
• Previous message: Giacomo Fiorin: "Re: well-tempered metadynamics deforms the water box and the system becomes unstable.."
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:10 CST