[AMBER] How to Compare RDFs for different systems

From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Date: Sat, 30 Oct 2021 17:15:01 -0400

Dear Amber Community,

I want to compute the radial distribution function for solvent relative to a cofactor for a monomeric and dimeric protein system. I don’t fully understand the comments about the care needed for normalization at https://amberhub.chpc.utah.edu/radial-rdf/ <https://amberhub.chpc.utah.edu/radial-rdf/>. My two systems have different numbers of solvent molecules, but if the raw RDF is normalized for each system with the default density value in CPPTRAJ, why would the two RDFs not be comparable? Or, put another way, how can you compute RDFs for two systems with different numbers of solvent molecules so that they can be compared?

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Received on Sat Oct 30 2021 - 14:30:02 PDT
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