[gmx-users] how can I obtain the potential energy of each atom？

[Justin Lemkul]

On 4/29/19 4:29 AM, Zhang Ke wrote:
> Hello Sotirios,
> Thanke you for your suggestion! I had attempted to use gmx_energy with 
> the index of each atom as an input. However, gmx_energy just contains 
> the interaction energy between the groups and doesn't contain the 
> output of the potential energy of the group.
>

gmx energy has no ability to produce such output, nor does any other 
GROMACS tool. How would one define the energy of an atom when all 
properties depend on pairwise bonded and nonbonded interactions? I think 
any result would have no physical meaning, particularly because no force 
field considers such a quantity (which sounds inherently quantum) in its 
derivation.

-Justin

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Justin A. Lemkul, Ph.D.
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