[gmx-users] Umbrella Sampling

Steven Neumann s.neumann08 at gmail.com
Sun Feb 12 01:48:00 CET 2012

Dear Gmx Users,

I run a simulation of a protein and 10 ligands. They all stacked on the
protein surface. I extracted the coordinates of the somplex and I am doing
Umbrella Sampling - I am trying to pull one of the ligand from my protein.
My questions:
Would you suggest restarining positions of the protein (and 9 other
ligands?) when pulling my ligand?
Would you restrained positions of the protein when running simulations in
each window?
How do you adjust the pulling constant force? Is there any rule or you just
change it and observe?

Thank you,

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