From: Artur Hermano (artur.hermano_at_hotmail.com)
Date: Tue Jun 12 2018 - 10:28:28 CDT
Hi namd users,
I've been running ABF simulations with a protein-protein complex, and even with stratification my analysis continues to show nonuniform sampling of forces acting along the reaction coordinate (distance between the two proteins). The sampling becomes uniform only when the PMF reaches a plateau, but before this point the sampling has many peaks and troughs. Why does that happen? If the FABF is applied only when the number of forces accrued in each bin reaches a threshold, wasn't this number supposed to approximately the same in every bin?
I wonder if this could spoil my free energy analysis and how could I modify the starting files in order to get a more uniform sampling. Do you have any suggestions? I'd very much appreciate any! Thank you!
-- Artur Hermano Mestrando em Biologia Computacional e Sistemas Instituto Oswaldo Cruz
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