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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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