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. Author manuscript; available in PMC: 2022 Jul 20.
Published in final edited form as: J Chem Theory Comput. 2022 Apr 6;18(5):3231–3238. doi: 10.1021/acs.jctc.2c00058

FIG. 4:

FIG. 4:

Time series data for (a) 500ns unbiased MD started from a configuration with BA placed outside the membrane, and SPIB based metadynamics, (b) free energy along (d1Z, θZ) for biased simulation. (c) two converged SPIB states depicting key permeation barrier. Permeation mechanisms are highlighted in (d, e, f) where in respective cases, BA has found an entry point into the membrane, is stuck at the surface along +Z direction, and is stuck at the surface along −Z direction from membrane COM.