[gmx-users] Docking using MDS

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 1 11:50:59 CEST 2008

vivek sharma wrote:
> Hi There,
> I am trying to run MD simulation for screening  my docking result, but I 
> am not aware of what are the parameters and analysis we can do for 
> docking by using MD simulation.

That depends entirely upon the scope of your question and what you want to 
learn.  Are you running MD on docked configurations, or are you trying to study 
ligand binding by MD?

What is it that you are trying to investigate?  This question will largely 
motivate what type of analysis you do.


> If anybody have tried the similiar things using GROMACS, Please help me 
> in this regard.
> With Thanks,
> VIvek
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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