Obtaining molecule-level kinetic energy/temperature info after the simulation has finished running

[alevilla]

Hi,
To get the temperature, a critical point to properly account for constraints. Maybe this link help
https://manual.gromacs.org/current/reference-manual/algorithms/molecular-dynamics.html)

Also the following discussions, may be useful to cross check your approach.

How can I obtain the temperature of a specific group?

GROMACS version: 2018.8 Hello everyone, my system is a composite, I need to calculate the temperature of a certain group of atoms. I searched a little and have found this post. I also read the doc pages and tried both methods mentioned in that post, i.e. gmx traj -ot and gmx mdrun -rerun with .tpr and .xtc files of that group of atoms. But the problem I found is the same as that asked in that post, the temperature obtained is consistently lower. I set the temperature of that group to be 300 …

Calculation of kinetic energy from velocity and mass information

GROMACS version: 2018.1 GROMACS modification: No Hello dear GROMACS users and developers, I fall into trouble during some consistency check of my molecular dynamics trajectories. I found out I am not able to reproduce the proper value of kinetic energy of the system. The value I get from gmx energy tool (~6952 kJ/mol) and the value I calculate from mass (tpr file) and velocity (trr file) data differs significantly. Thus I would rather start with a snippet of a python code (utilizing MDAnalysi…

\Alessandra