[gmx-users] Umbrella sampling

rose rahmani rose.rhmn93 at gmail.com
Thu Jun 28 15:56:06 CEST 2018


I do umbrella sampling for different distances of AA along surface and i
calculated error by bootstrapping method. Error is less than 0.5 kj.mol-1
in 0.8to1.7 nm far from surface, but in 0.6to0.8 nm error is about 2
kj.mol-1 . The minimum energy is about -5kj.mol-1 at 0.65 nm. All windows
overlapped in histo plot.
So how should i know that this error is neglectable or not? I did sampling
many times but near surface, the error is too much and windows have
significant overlapping and count is about 2 times higher than 0.8 to 1.7
Would you please help me? Is there any criteria other than overlapping and
estimating error i should notice to?

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