Dear Amber Community,
Is there a way to visualize the grid of points where the implicit solvent is being evaluated?
I am running constant pH and redox simulations, and I suspect that one of the redox potentials is significantly wrong (too negative) because the implicit dielectric is being placed where it ought not go. If I let all pH and redox active groups be titratable, the redox potentials for two of the three heme cofactors in my system come within 5 meV of the experimental values, which themselves have a 5 meV error bar. The third heme, however, has a redox potential that is more negative compare to experiment by ~150 meV (absolute value = -266 meV).
Even if there is nothing I can do to remedy the discrepancy, I would still like to assess by some means if this hypothesis is right, or if something else is amiss.
Best regards,
Matthew
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Received on Thu Aug 05 2021 - 01:00:02 PDT
