[gmx-users] Umbrella Sampling application

Steven Neumann s.neumann08 at gmail.com
Fri Jan 13 14:32:49 CET 2012

Dear Gmx Users!

I do protein-ligand simulations and I am interested in binding free energy.
My ligand is not charged molecule, there is no specific binding so hydrogen
bonding and hydrophobic interactions are responisble for binding. I have
experimental data from ITC of binding free energy.

I am wondering whether application of Umbrella Sampling would be a good
aplication. I would like to put e.g. 10 ligands around my protein (200
residues) and see which of them went into my structure deep (stronger
interaction) and then using position restrained dyunamics of my protein and
other ligands pull crucial ligand and perform windows for Umbrella Sampling
then obtaining free energy?

The second thing I would like calculate is binding free energy of the
second "layer" of ligands - I mean: they do aggregate one on the another,
so in this case will Umbrella Sampling can be used to pull ligand from the
another which stacked to my protein (posre of my protein and 1other

The third thing I am interested is chemical potential of my ligand in this
system. Can you please suggest some technique to obtain it - further
reading, tutorials?

Thank you in advance,

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