FORECASTING MOLECULAR DYNAMICS SIMULATIONS OF POLYMER-LIPIDS IN SOLUTION WITH RNNs

Files and scripts pertaining to our work: 

GROMACS files for the topology (DSPE+PEG.top) and the initial structure of the aggregate (DSPE+PEG_EA_NPT.gro)

GROMACS topology file for the ethyl acetate molecule: EA_SI.top

Scripts to submit the GROMACS utilities for calculation of the interaction energies are described in README.txt (Subset_energy.sh , Interaction_energies.sh)

Scripts pertaining to PyTorch use and access of methods are described in README.txt (Multiple-run.sh. Job.sh, Pytorch_train-model.py)

Scripts pertaining to scikit learn access for the Expectation Maximization clustering are described in the README.txt (Job_EM.sh, EM_Clustering.py)

Files with the time series of the potential energy (PE) and interaction energy (IE) of the DSPE-PEG aggregate with the ethyl acetate solvent. Series contain 500,000 snapshots taken every 10 fs along the NVT Molecular Dynamics trajectory at 300 K and 906.3 kg/m3 density. The molecular solution is in a cubic box of edge length 13.76 nm, containing 16,000 ethyl acetate molecules and one aggregate of 4 DSPE-PEG-amide macromolecules (224,000 atoms): Data_Andrews_etal_DSPE-PEG_2022.zip

ArXiv preprint: https://doi.org/10.48550/arXiv.2203.00151 (JAndrews_etal_arXiv-doi.pdf)