How to Calculate Energies for "Specific" Atoms?

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GROMACS version: 2022.1
GROMACS modification: No

We have developed a highly crosslinked polymer system. Initially, the system consisted of a large main chain and other smaller chains, which we referred to as free chains. These free chains were not connected to the main chain. After identifying all the free chains, we removed them from the system.

I previously extracted atom indices for calculating dihedral autocorrelation, but now I want to move on to energy analysis. Specifically, I am interested in calculating Dihedral, Van der Waals, Bond Stretching, Angle Bending, and Electrostatic energies near the crosslinking points. I have already extracted the atom indices of the crosslinking points, as well as the indices of the four atoms involved in the dihedral interactions.

Given that I have these index files, how can I calculate the energies between the atoms near the specific crosslinking points using GROMACS or similar tools?

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This can not be done in GROMACS, apart from by generating a topology where all other interactions are not present or have parameters set to zero.

Note that in many cases looking at potential energies is not useful. It is the free-energy that governs the states of the system and that includes entropy.

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Thank you for your comment. I found that using the ‘mdrun -rerun’ option after creating a new ‘.trr’ file resolves the issue.