Comments (2)
Great project.
Here is some information may be relevant:
https://arxiv.org/abs/2003.00868
https://frankschae.github.io/post/shadowing/
basically, the automatic differentiation through a trajectory generated by a stiff differential equation (MD simulations can be considered as this kind), chaos can not be avoided which causing the gradient becoming useless. It gives huge difficulty to optimize parameters based on MD trajectory.
Another thing can be done is probably to add stochastic terms (langevin thermostat) in the MD system, some tests can be found in this paper https://arxiv.org/abs/2301.03480.
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Thanks for your sharing !!!
I am currently dealing with this problem, and I will pay attention to these works. Hope I can discuss with you when I have some thoughts on this.
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Related Issues (20)
- [Feature Request] Request a new feature for development of reactive force field HOT 3
- [BUG] spatial.py shape error
- Question about gradient HOT 7
- [Feature Request] Change the API of polarizable potential (ADMP and Qeq) functions HOT 1
- [Feature Request] Change the default unit of the ADMP frontend
- [BUG] Out of Memory Issue During Neighbor List Generation HOT 2
- [BUG] Matching energies to reference after dynamics HOT 2
- [Feature Request] Install dependencies automatically and publish to PyPI HOT 3
- [Feature Request] Support for machine learning force field in OpenMM DMFF plugin HOT 1
- Installation problem
- Op type not registered 'XlaSharding' in binary running HOT 1
- [Feature Request] Refactor the cpp interface of the saved DMFF jax model with MD engine
- update the charge HOT 2
- [BUG] LJ switch function
- [Feature Request] Support Virtual Site in DMFF frontend HOT 1
- [Feature Request] MD Engine Support (LAMMPS) for trained model with DMFF
- [Feature Request] QEQ modelโs parameterization for conductive electrodes with DMFF HOT 1
- [Feature Request] Workflow to fit relative protein-ligand binding free energy data
- [Feature Request] Efficient neighborlist construction/usage plugin for nonbonded force calculation HOT 1
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