[gmx-users] Umbrella sampling-protein-ligand complex

Justin Lemkul jalemkul at vt.edu
Fri Sep 28 20:20:41 CEST 2012

On 9/28/12 2:19 PM, Archana Sonawani wrote:
> Dear Justin,
> So do I have to carry out umbrella sampling simulations separately for the
> three complexes or put the three ligands together with the protein and pull
> the ligands one by one to calculate the binding energy. I am confused.

Each complex has to be treated separately.  Simultaneously pulling three 
molecules won't make any physical sense and the simulations would crash anyway.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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