GROMACS version:gromacs 2021.1
GROMACS modification: No
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I used the gmx traj command to try to analyze the temperature and energy of individual components in a multi-component mixed system simulation. However, as shown in the figure below (see figure “Etrans calculated with gmx traj”), the translational kinetic energy did not increase even though the temperature increased over time.
Therefore, for verification, the temperature and translational energy were calculated from the atomic velocity information by the self-made program created according to the equations (7) to (11) described in the following links(Molecular Dynamics — GROMACS 2021.1 documentation). The calculation results are shown in the figure “Etrans calculated with self made program”. From this result, I realised that the translational kinetic energy shows the same tendency as the temperature, so I doubt the calculation result of gmx traj.
In addition, the rotational energy calculated using the gmx traj command (see figure “Erot calculated with gmx traj”) is several orders of magnitude larger than the translational energy, and I’m not sure if this value is valid.
I would appreciate any advice on these issues.