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
--
========================================
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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