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Overview

  1. bent-int1: Contains generated 300 CG bead structure using cWGAN and the corresponding predicted all-atom structure using targeted MD simulations between bent and int 1 state.
  2. bent-int2: Contains generated 300 CG bead structure using cWGAN and the corresponding predicted all-atom structure using targeted MD simulations between bent and int 2 state.
  3. bent-open: Contains generated 300 CG bead structure using cWGAN and the corresponding predicted all-atom structure using targeted MD simulations between bent and open state.
  4. int1-int2: Contains generated 300 CG bead structure using cWGAN and the corresponding predicted all-atom structure using targeted MD simulations between int 1 and int 2 state.
  5. int1-open: Contains generated 300 CG bead structure using cWGAN and the corresponding predicted all-atom structure using targeted MD simulations between int 1 and open state.
  6. int2-open: Contains generated 300 CG bead structure using cWGAN and the corresponding predicted all-atom structure using targeted MD simulations between int 2 and open state. In 1-6, each folder contains subfolders named target_md_int1_0 to target_md_int1_9 and target_md_open_0 to target_md_open_9. target_md_int1_* contains all-atom structures generated using int 1 all atom structure as the initial structure in targeted MD simulations. Simularly, target_md_open_* contains all-atom structures generated using open all atom structure as the initial structure in targeted MD simulations. 0 to 9 refer to the ten structures generated between the states as shown in the paper.

NOTE: Because each file is ~2.5 MB, the data is uploaded using git lfs. To download the structures, it may be better to simply download the entire repository as a zip file.

Notebooks

cg_300_integrated_training_integrin_dmap_decoder-generatePoints.ipynb: Notebook to generate the ten latent space points between metastable states and generate the 300 bead CG structures using the trained cWGAN model.

cg_300_integrated_training_integrin_dmap_decoder-generatePoints.ipynb: Notebook to generate 300 bead CG configurations at any given latent space point. In this notebook, the configurations are generated to generate potential structures along switchblade and deadbolt mechanism.

GROMACS + PLUMED FILES

master_tmsd contains template GROMACS mdp and PLUMED files used for setting up the targetted MD simulations. Scripts to launch the simulations are prep-sub.sh and sub.sh. Force field and initial all atom reference gro files are located in all-atom folder.