Calculate energy, temperature and pressure for separate parts of the system

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GROMACS version: 2020.1
GROMACS modification: No
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Dear Gromacs users,

I am a Beginner.

I am trying to simulate DNA on Diamond in water.

I am supposed to analyze energy, pressure and temperature separately for the DNA and for the diamond.

But gmx energy does not support .ndx files like -n DNA.ndx or -n Diamond.ndx as input options.

Could anybody give me a hint on how to proceed?

Thank you so much and best Regards,
Stefan

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You can get the temperature of different groups using tc-grps in the .mdp file, but this also implies that they will be coupled individually to the thermostat, so they’ll basically always be at the desired temperature. But that’s likely the case anyway.

Pressure is not decomposable in the way you want.

You can calculate the energy of a given group by extracting the subset of atoms from the trajectory with trjconv, creating a matching .tpr file with convert-tpr, and re-calculating the energy with mdrun -rerun but this will (1) only be the potential energy and (2) the quantity has no physical meaning since force fields aren’t parametrized to make such things meaningful.

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Thank you so much :)