Update README.md

README.md

@@ -6,4 +6,47 @@ license: mit
 
 This dataset contains molecular dynamics simulation data that was used to train the neural networks in the NeurIPS 2023 paper [Timewarp: Transferable Acceleration of Molecular Dynamics by Learning Time-Coarsened Dynamics](https://arxiv.org/abs/2302.01170).
 
-This dataset consists of many molecular dynamics trajectories of small peptides (2-4 amino acids) simulated with an implicit water force field.
+This dataset consists of many molecular dynamics trajectories of small peptides (2-4 amino acids) simulated with an implicit water force field. 
+For each protein two files are available:
+
+* `protein-state0.pdb`: contains the topology and initial 3D XYZ coordinates.
+* `protein-arrays.npz`: contains trajectory information.
+
+The datasets are are split into the following directories:
+
+# 2AA-1-big "Two Amino Acid" data set
+
+This folder contains a data set of all-atom molecular dynamics trajectories for 380 
+of the 400 dipeptides, i.e. small proteins composed of two amino acids.
+This dataset was orginally created missing 20 of the 400 possible dipeptides.
+The `2AA-1-complete` dataset completes this by including all 400.
+Each peptide is simulated using classical molecular dynamics and the
+water is simulated using an implicit water model.
+The trajectories are only saved every 10000 MD steps. There is no intermediate
+spacing as for the other datasets for the Timewarp project.
+
+# 2AA-1-complete "Two Amino Acid" data set
+
+This folder contains a data set of all-atom molecular dynamics trajectories for all 400
+dipeptides, i.e. small proteins composed of two amino acids. 
+This includes also the peptides missing in the other 2AA datasets.
+Each peptide is simulated using classical molecular dynamics and the
+water is simulated using an implicit water model.
+
+# 4AA-huge "Four Amino Acid" data set, tetrapeptides
+
+This folder contains a data set of all-atom molecular dynamics trajectories for
+tetrapeptides, i.e. small proteins composed of four amino acids.
+The data set contains mostly validation and test trajectories as it was mostly
+ used to validation and test purposes.
+The training trajectories used are usually shorter.
+Each peptide is simulated for 1 micro second using classical molecular dynamics and the
+water is simulated using an implicit water model.
+
+# 4AA-large "Four Amino Acid" data set, tetrapeptides
+ 
+This folder contains a data set of all-atom molecular dynamics trajectories for
+2333 tetrapeptides, i.e. small proteins composed of four amino acids.
+The data set is split into 1500 tetra-peptides in the train set, 400 in validation, and 433 in test.
+Each peptide in the train set is simulated for 50ns using classical molecular dynamics and the
+water is simulated using an implicit water model. Each other peptide is simulated for 500ns.