[gmx-users] QM/MM energies

Christoph Riplinger cri at thch.uni-bonn.de
Fri Nov 25 16:57:58 CET 2011

Dear Jon,

To the best of my knowledge the potential energy is the sum of all 
energies (E_QM + E_MM + E_QM/MM). The quantum energy (actually I do not 
see it in my output) for electrostatic embedding includes E_QM + 
E_QM/MM(el.stat.). I.e. E_QM/MM(VDW) you have to extract from the edr 
file. You should have two different energy groups, one defining the QM, 
and the other one defining the remaining system. I.e. you can extract 
E_QM/MM(VDW) from the sum of LJ-SR:notQM-QM and LJ-14:notQM-QM.

Importantly, if you want to analyze the QM_part of the energy, you 
should (i) either calculate E_QM without the point charges again, or 
(ii) add E_QM/MM(VDW) to the printed quantum energy (i.e. calculate E_QM 
+ E_QM/MM), since the electrostatic QM/MM contribution is included in 
the quantum energy for electrostatic embedding, and it is highly 
dependent on the  respective VDW contribution.

Hope that helps,
Christoph Riplinger

On 11/25/2011 11:08 AM, Jon Mujika wrote:
> Dear gmx users,
> I am performing some QM/MM optimizations using the ORCA interface in
> order to compare the energies of different structures of the same
> system. However, I have some questions related with the energy terms.
> In the output file the "potential" and "Quantum Ener." terms are
> printed out. The question is: does the Potential term include the QM
> energy? That is, is the "potential" energy the total QM/MM energy, or
> only the MM part of the total energy? On the other hand, since I am
> using the electronic embedding approach (QMMMscheme=normal in the .mdp
> file), I assume that the QM/MM electrostatic energy is included in the
> QM term. Is that correct? And what about the QM/MM van der Waals
> energy?
> I ask so because I try to calculate the potential energy from the
> different terms provided in the output, but I can't reproduce the
> potential energy.
> Thanks for you help
> Jon

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