Ye Ding

icon indicating a website link https://dingye18.github.io icon indicating an email [email protected]

icon location Beijing, China icon location PhD of Computational Biophysics. Graduate from School of Life Sciences, Westlake University. Currently working at ATOMBEAT.

Results 3 issues of Ye Ding

DP Mask Model

3 comment

I implement a DP Mask Model with self-defined `se_a_mask` op and `EnerForcesMaskLoss`. The main contribution comes from two points. 1. Add the argument for `mask_matrix.npy` (shape [num_frames, num_tot_atoms]), used in...

Python
Core
OP
C++

[Feature Request] Refactor the cpp interface of the saved DMFF jax model with MD engine

### Summary Moving the `jax2tf` to `HLOModule` for the cpp interface of the saved DMFF model. ### Motivation The current implementation of the cpp interface between the saved DMFF model...

enhancement

Charge in consistency between the files in gromacs_solvated.tar.gz and gromacs.tar.gz

5 comment

I just found that that atomic charges of part of the molecules are different in gromacs_solvated.tar.gz and gromacs.tar.gz. Such as the mobley_820789, the atomic charges in gromacs/mobley_820789.top are: While in...