[gmx-users] Re: Re: Re: Calculation of binding enthalpy in

Jong Wha Lee jongwha12 at postech.ac.kr
Tue Sep 24 03:21:35 CEST 2013

Dear Vitaly,


Thank you very much for your reply. I originally asked the question because
I wasn't sure my values were from correct procedures. Now I see how I could
properly calculate binding energies with MM.


John Lee


> Dear Vitaly,




> Thank you for your suggestion.




> I have also tried calculating interaction energies by specifying 

> energygrps in .mdp file, but calculated energies deviate greatly from 

> QM calculated energies and experimental results. I suspect that the 

> structure of each component in complex differs from the structures 

> when they were alone, because this will lead to a deviation in 

> equilibrium binding enthalpy from the interaction energies that is 

> calculated with energygrps line in .mdp file.



This might be because of electrostatics treatment method. Use simple cut-off
scheme and specify a really large cut-off radius, which exceeds the sum of
the sizes of your binding particles.


I made tons of such comparisons, QM vs. MM. It works pretty well.





> My guest of interest have two charges at a short distance, which is 

> very unfavorable and the charges will try to be furthest apart. 

> However, my host molecule can stability the charges via oppositely 

> charged groups, and so now the guest molecule forms a bent structure. 

> In this case, shouldn't the change in energy due to the different 

> conformation of the guest be taken into account, to discuss 

> equilibrium binding enthalpy? I feel maybe this wouldn't be well
represented with interaction energies.



The binding energy is an energy gain, dE, in the following reaction A + B ->
AB, dE


A, B, and AB are optimized geometries: in vacuum, in solvent or anywhere.
So, if a molecule changes its conformation during binding, this energy
gain/loss should be a part of the binding energy, I see no methodological
problem here.



Dr. Vitaly V. Chaban


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