Question about the units used in AToM

Gallicchio-Lab / AToM-OpenMM

OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method

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Question about the units used in AToM #92

Closed syxchen closed 2 months ago

syxchen commented 2 months ago

Hi!

I am new to OPENMM and I have a question regarding the energy unit used in the software. As far as I know, the default energy unit in OPENMM is kJ/mol. I am wondering if the AToM scripts convert the energies to kcal/mol when calculating the binding free energy (ddG), or if the ddG value provided by AToM is in kJ/mol? Any clarification would be greatly appreciated!

egallicc commented 2 months ago

AToM-OpenMM uses kcal/mol energy units and Angstroms for distances.