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 MDAnalysis package) I am using for the data calculation rather then describing the details of the system as I must be missing something elementary.

```
import MDAnalysis as MD
import numpy as np
mass_conversion = 1.660538921*1e-27 # convert atomic mass to kg
speed_conversion = 1e3 # convert nm/ps to m/s
N_a = 6.02214076*1e23 # Avogadro's number
topo_file = MD.topology.TPRParser.TPRParser('diala_water.tpr')
trajectory = MD.coordinates.TRR.TRRReader('diala_water.trr')
topo = topo_file.parse()
vel_arr = trajectory.ts.velocities
mass_arr = topo.masses.values
nof_particles = topo.n_atoms
nof_residues = topo.n_residues
sum = 0
for i in range(nof_particles):
sum += mass_arr[i] * np.linalg.norm(vel_arr[i, :])**2
kin = sum / 2 * mass_conversion * speed_conversion**2 * N_a / nof_residues
print('Kinetic energy %.2f kJ/mol' % (kin/1000))
```

If i didn’t make a mistake in a code it is suppose to make a sum of “m_i*|v_i|^2” term over all atoms in the simulation box. Where m_i is mass and |v_i| the norm of velocity of particle i. Then take a half of this sum and multiply it by conversion factor due to mass and velocity units. Last step taken was to evalute the energy per mol. Though this was a source of a little confusion for me as I am not sure whether the value given by gmx energy tool is given as of mol of atom or molecules I tried to recalculate the value for both possibilities. And I get the values 247.58, 747.56 and 654117.50 kJ/mol in case of mol of atoms, mol of residues and mol of simulation boxes. Can you please give me a hint how to get the proper value? Thanks in advance! Jiri