[gmx-users] Umbrella Sampling - spacing

Steven Neumann s.neumann08 at gmail.com
Wed Feb 22 17:03:48 CET 2012

Dear Gmx Users, Dear Justin,

I run pulling of my ligand away from my protein. Then I used Justin perl
script to extract distances for umbrella sampling windows between my ligand
and crucial residue of my protein (Isoleucine). The number of hydrogen
bonds between ligand and protein during the pulling is app. 3 at the
begining, then 4 in some frames and then obviously zero (when ligand
Would you use the 1st frame as a starting window when number of hbonds is 3
or further window when this is number is 4?
Is spacing of 0.2 nm (pulling of app 6 nm) sufficent for the system where
interactions are via hydrogen bonds and hydrophobic interactions only?

Thank you.

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