[gmx-users] umbrella sampling distances

Irem Altan irem.altan at duke.edu
Fri Nov 18 04:06:48 CET 2016


I’m trying to apply umbrella sampling to a system following Justin Lemkul’s tutorial. I’m confused about how the distances are calculated, however. When I run a pull simulation and calculate center of mass distances with gmx distance, I see that the distance in the 0th configuration is 3.003 nm. When I look at the output PMF generated with gmx wham, the PMF starts from 2.56 nm. What could I be missing?


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