From: Alex Hummels (alexhummels_at_me.com)
Date: Thu Jul 02 2020 - 17:19:11 CDT
I’m trying to setup a REST2 simulation and I was curious about the soluteScalingFactor.
First off, and this is more curiosity than anything, is there not a default value for soluteScalingFactor? It would make sense to me that by default you would have beta be 1. However the NAMD page on Solute Scaling and REST2 does not mention a default value for soluteScalingFactor. Or am I just missing the point and beta should always be less than 1 and the user will just have to set it themselves since there’s not an agreed upon number less than 1?
Second, in looking at the powerpoint by Wei Jiang about REST2, there are suggested values given for soluteScalingFactor, as well as soluteScalingFactorCharge and soluteScalingFactorVdw, but are referred to as “flexible for different systems". For context, I am trying to use REST2 to look at the interactions of disordered proteins on top of a self-assemble monolayer (SAM) with an explicit solvent. The total system contains over 138,000 atoms. Does anyone know if this setup would require different parameter values than the 0.9, 0.8, and 0.7 suggested for the factor, charge, and vdw parameters? I just want to make sure I start running simulations that nothing about my system would call for modified parameters.
Thanks in advance for your help,
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