Hi Nelly Coulonges

Take a look here, it might help you! :)

https://manual.gromacs.org/documentation/2019/reference-manual/definitions.html#reduced-units

Thank you for the link, it is indeed helpful !

Just a question to be sure that I understand. When it says "if a reduced temperature of 1 is required, the GROMACS temperature should be 120.27236", does "a Gromacs temperature" mean that the temperature I will set in Gromacs is in the standard unit system, meaning in Kelvin ?

I am not completely sure I can answer/I understand here. I think GROMACS is expecting the temperature in K as everything (forces etc) are written in the standard MD units reported in the paragraph before

https://manual.gromacs.org/documentation/2019/reference-manual/definitions.html#md-units

If you need you can use reduce units which seems to be consistent as long as you use a simple LJ potential and you use the scaled terms. The only part which is a problem is the temperature, where you should consider the conversion term. So, I guess you are really saying to the code "fix the temperature at 120.27236 K" but, given the change in the energies, it is equivalent to ask for T=1 in reduced units. So it's a workaround as you can't change the units of the temperature?

I guess you can try and see if you can reproduce a simple phase space diagram of a LJ liquid and see if it is consistent with what you have in literature. I think also the input structure should also be in units of sigma? Personally, I would stick to the standard units (so convert the LJ reduced ones to the GROMACS ones) and re-convert later the length/energies etc, as I am pretty sure I would mess up something somewhere. I think this might be also a good benchmark. Try a reduced unit sim and a "normal sim" where you convert the LJ reduced terms to GROMACS ones. If the two outputs are the same then you are confident in your reduced units sim.

Thanks a lot for the detailed answer. I will run simulations in Gromacs units, because as you said I will probably mess up something somewhere with the reduced units.

I am still unsure if I understand fully though. My fear is that Gromacs recognizes my temperature as Kelvin, but since I did set my length parameter to 1, the velocities are rescaled differently and therefore what Gromacs "thinks" is 120K is actually not (in the sense that the relation between velocity and temperature is not respected). But I guess I will just run everything in "normal" units and that should solve my problem.

That's a good point. The potential energies you compute are in reduce units if you provided reduced units in the definition of the potential. So I think the derived forces will be in reduced units (and as such you should interpret/provide the starting box thinking of positions as if rescaled by sigma)?

The kinetic energy should go as the degrees of freedom (adim), the masses (reduced), and the squared velocities. The correction the thermostat applies is a dampening which I think can be considered adimensional as you can see here

https://manual.gromacs.org/nightly/reference-manual/algorithms/molecular-dynamics.html#velocity-rescaling-temperature-coupling

but then I guess the coupling time should also be provided in reduced units? Which actually leaves open the question of which timestep should I adopt for integration.

By looking at the manual when it reports the reduced units it seems that really just reporting the LJ parameters as reduced will fix everything (except for temperature). Honestly I believe your route is the safest, as the conversion needs to be done once in the parameters and then you are okay wrt the simulation, while all the rest is a simple matter of unit rescaling while analyzing the output. I guess also trying once with reduced and once with all converted and checking that the results are identical would give you confidence in the reduced approach.

I ran simulations with standard units, and I could calculate the temperature without problem. So I concluded that my problem came from my own calculations when converting from reduced units back to standard units. And indeed, my problem lied in the fact that when converting velocities, I was only multiplying by sigma, forgetting that the unit of time was also modified. I multiplied my velocities by sqrt(epsilon/M) and could recover the right temperature