Hi,
I ran some MD simulations in GROMACS and am trying to get a sense of the changes in potential energy of the active site between conditions (with and without inhibitor present). I have defined indices (.ndx) with the appropriate residues in the active sites, and have successfully generated an .xtc file with energies for those residues. However, I only am finding the coulombic and LJ potentials. Is there a way to also get bonded terms, or am I just not seeing it in the output?
You should see a term named Potential when you run gmx energy -f md.edr
Even if you don't define anything in your energygrps you should obtain all the potential terms anyway
You can only get such an output by using mdrun -rerun on a trajectory that has been stripped of everything except what you want, which also requires a matching .tpr file (made with gmx convert-tpr).
Bonded terms are not subject to energygrps, which call only for the decomposition of short-range nonbonded interactions.
Be careful trying to compare bonded terms, as changes in geometry can quickly lead to comparing apples and oranges.
To those suggesting energygrps, that's not how that keyword works. It is not for the selection of energy terms, it is for the specification of groups of atoms (specified in the index file) for which the short-range nonbonded interaction energy is decomposed in a pairwise manner.
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