ABF protocol to calculate PMF

From: Rukhsar Ali (arukhsar052_at_gmail.com)
Date: Wed Aug 12 2020 - 11:13:53 CDT

I'm very new to the ABF protocol to calculate PMF. I'm wondering, if I want
to calculate a backward PMF for a peptide insertion process into a bilayer,
should I just pick initial structures near the lower boundary end state for
each window and run the same simulations as in forward PMF calculations? I
mean, for a window 10A-12A (along 'distance Z' colvar), I have taken the
initial structure around 12A during forward PMF calculation. So now, for
the backward PMF, should I just take the initial structure near 10A?


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