PMF calculation using ABF

From: Souvik Sinha (
Date: Tue May 10 2016 - 08:57:52 CDT

I am trying to get the energy landscape along a specific reaction
coordinate(RC) for my system using COLVAR assisted ABF protocol. Each of
the stratified windows along the RC is sufficiently sampled (20ns) as I
have checked the convergence of the final PMF plot. As there was an unusual
steep rise in the plot, I have decided to repeat the calculation for a
check. But, after the second run for the same no of steps, the calculated
PMF is something different from the previous run. Convergence is still
there, though the minima & maxima have been clearly shifted. I didn't
expect different nature of energy landscapes from independent runs. Can
anyone help me with a possible explanation?

Souvik Sinha
Research Fellow
Bioinformatics Centre (SGD LAB)
Bose Institute
Contact: 033 25693275

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