From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Wed Feb 13 2019 - 15:20:02 CST
As far as I can tell, soluteScaling has no effect on the electrostatic
energy, despite the NAMD manual indicating that it should.
The NAMD 2.13 manual says:
soluteScalingFactorCharge Solute scaling factor for electrostatics
Description: Scaling factor applied to just the electrostatics
interactions. If not specified, this is set to soluteScalingFactor.
soluteScaling has no effect on the electrostatic energy, whether I
specify soluteScalingFactorCharge or not. On the other hand, I find
that the VDW and dihedral energies energies scale as expected. I'm
using a recent NAMD build (NAMD_Git-2019-02-01).
I also tried with "soluteScalingAll on". Then, the bond energy scales
as expected. Urey-Bradley angle energies apparently do not scale;
however, this doesn't cause any bad behavior.
On the other hand, I find what I might term "bad behavior" of
soluteScaling when NBFIX parameters are applied. Applying
"soluteScaling on" and "soluteScalingFactor 1.0" (which should have no
effect) causes changes in the total energy of the system when NBFIX
terms are included. The soluteScaling code evidently overrides any
NBFIXes that are active without any warning. Because NBFIXes between
sodium ions and protein carboxylates are part of the standard CHARMM36
force field for proteins (which I think of as the prototype force
field for NAMD), I would like to see them supported by soluteScaling.
If not, at least there should be a warning that NBFIXes are no longer
applied when soluteScaling is active.
Jeffrey Comer, PhD
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
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