Protein in explicit water solvent box simulation with Jax_amber

[Byun-jinyoung]

Is is possible to run MD simulation a large protein (AA>300) in explicit water solvent with Jax_amber?

[swillow]

Thank you for expressing your interest. Indeed, it is possible to add the requested feature, and I will make sure to incorporate it soon. However, if your sole purpose is to run molecular dynamics (MD) simulations, I would recommend utilizing OpenMM or other advanced software packages. It is worth mentioning that I developed "jax_amber" primarily for a project centered around deep machine learning.

[Byun-jinyoung]

Thank you for you reply! I'd like to simulation protein in explicit solvent with MD + deep learning approach (e.g. roughly such as OpenMM + openmm-pytorch although I've never used openmm-pytorch...). Thus my first idea is combination (JAX_MD in explicit solvent + 'JAX NN potential deep learning') for sampling rare event or exploring conformational space more efficiently because JAX support autodifferential. What do you make of it?

[swillow]

Please check the directory 'periodic_system'.