Denoising diffusion model for coarse-grained molecular dynamics

A method for use with a computing system, the method comprising;

• receiving atomistic molecular dynamics simulation data of a plurality of training-time conformers of an atomistic structure of a molecule;
• computing coarse-grained molecular dynamics simulation data of the molecule based at least in part on the atomistic molecular dynamics simulation data, wherein the coarse-grained molecular dynamics simulation data is computed at least in part by converting the atomistic structure into a coarse-grained structure of the molecule;
• training a denoising diffusion model using the coarse-grained molecular dynamics simulation data;
• at the denoising diffusion model:
• receiving a runtime conformer of the coarse-grained structure;
• and
• generating a coarse-grained force field estimate associated with the runtime conformer;
• outputting the coarse-grained force field estimate to a molecular dynamics simulation module;
• and
• generating a molecular dynamics simulation of the molecule at the molecular dynamics simulation module based at least in part on the coarse-grained force field estimate.

A computing system comprising:

• a processor configured to:
• receive atomistic molecular dynamics simulation data of a plurality of training-time conformers of an atomistic structure of a molecule;
• compute coarse-grained molecular dynamics simulation data of the molecule based at least in part on the atomistic molecular dynamics simulation data, wherein the coarse-grained molecular dynamics simulation data is computed at least in part by converting the atomistic structure into a coarse-grained structure of the molecule;
• train a denoising diffusion model using the coarse-grained molecular dynamics simulation data;
• at the denoising diffusion model, generate a plurality of independent identically distributed (i.i.d.) samples from an equilibrium distribution of the coarse-grained structure;
• and
• output the plurality of i.i.d. samples.