Regarding the input file format for torchmd-net training of Amaro model

[SoumyaCYZ]

Respected Sir,
Hope you are fine and doing well. Currently, I'm learning amaro. I'm using alanine dipeptide for this purpose. I performed 500 ns equilibrium simulation at 300 and 320 K temperatures in GROMACS software. I have computed the force acting on each atom and the non-hydrogen heavy atom coordinates. Should merge the trajectory of 300 and 320 K temperatures before training. What data should I store in the DF5 file (specifically row and columns)?
Regards
Soumya

[SoumyaCYZ]

Respected Sir,
I have another doubt. Should I save the coordinates and forces of water molecules (specifically water's oxygen) to get a potential for both dipeptide and water to simulate in OPENMM-TORCH?
Regards
Soumya

[SoumyaCYZ]

@RaulPPelaez sir can you please help?

[RaulPPelaez]

@AntonioMirarchi you would know best here.