[gmx-users] Extract LJ-14 energy

[Justin Lemkul]

On 1/2/20 6:11 AM, Suvardhan Jonnalagadda wrote:
> Hi,
> Thanks for the reply. In the log file I could not find any 'LJ14' term, but
> 'LJ (SR) term is present.
>
> My molecule has 17 atoms, and there are 1-4 interactions.
>
> 1.) Is the LJ(SR) term not the same as LJ14, in my case, since I have only
> one molecule?

They are different. Depending on how your topology was constructed, 
LJ(SR) may encompass LJ14, but they are not equivalent.

> 2.) Also, how to see what 1-4 interactions gromacs has considered for the
> calculations? When I calculated for the molecule, manually, the 1-4 LJ
> contribution is mismatching.

Use gmx dump on your .tpr file. 1-4 interactions are computed for 
topologies with nrexcl = 3 and defined [pairs]. If you did not do this, 
you have no 1-4 energy term, but it will be computed as part of LJ(SR) 
unless nrexcl > 3.

-Justin

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Justin A. Lemkul, Ph.D.
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