[gmx-users] Coulomb and vdW energies

[Justin Lemkul]

On 11/30/19 3:14 AM, elham wrote:
> Dear all, I want to obtain the coulomb and vdW energies between two atoms of separate molecules, However  the .edr output calculate coulomb  and vdW energies of whole system. There is not any option(like -n .ndx) to define the the special atoms in the gmx energy command. How can I calculate the coulomb and vdW energies between the two atoms which are related to two separate molecules?Best

Set energygrps in the .mdp file, generate a new .tpr, and use mdrun 
-rerun to re-evaluate the energies from an existing trajectory. Note 
that decomposition of energy in this way has no physical meaning. Total 
interaction energy may be physically realistic if the force field was 
specifically parametrized against e.g. QM target data but decomposing 
the energy in this way is not meaningful.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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