GROMACS version: 2023.2
GROMACS modification: Yes/No
Are there any other indicators besides some measure of binding affinity that tell me whether or not I have my GROMACS simulation or my gmx_MMPBSA process correctly. For example, can the .xtc trajectory file output from my GROMACS simulation tell me if my protein-aptamer complex was preprocessed correctly for gmx_MMPBSA? What the geometry of the output .gro file or the .tpr file? I guess I am just looking for ways to validate my procedure and results.