There is something not quite right here. I grompp a gro file created from a pdb file using pdb2gmx and run MD to do a single point energy calculation.
I then grompp the original pdb file and run MD to do a single point energy calculation. The values of potential energy values are different by about 3 kJ/mol for a small molecule. These things should carry a "bad for your health" sign :D
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