[gmx-users] crude interaction energy using g_energy

[Justin A. Lemkul]

On 5/27/12 8:41 PM, sai nitin wrote:
> Dear all,
>
> Recently i performed  two 15ns simulation of  protein-ligand systems using
> gromacs of my interest...and using g_energy tool..i calculated crude
> interaction energy based on short-­‐range energy components Eint = <ELJ> +
> <ECoul>. ...I got two Eints for two simulations
>
> 1) Eint = -51.003 Kcal/mol (first simulation)
> 2) Eint = -26.615 Kcal/mol (second simulation)
>
> Can anybody tell me what meaning can i make out of it...means is first
> simulation is more stable than second one..or vice versa...
>

I don't think you can say anything about stability based on these figures.  In 
simulation 1, the interaction is more stable than in simulation 2.  It seems 
clear that the two simulations behaved somewhat differently, but the exact 
differences will only become apparent through other analyses and visualization.

-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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