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AD-3/README.md

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+# Alanine Dipeptide trajectory data
+
+This folder contains a minimal data set of two long MD trajectories for alanine
+dipeptide, the simplest dipeptide (22 atoms).
+
+For each trajectory two files are available:
+
+* `protein-state0.pdb`: contains the topology and initial 3D XYZ coordinates.
+* `protein-arrays.npz`: contains trajectory information.
+
+## NPZ Information
+
+The NPZ file contains detailed information for a subset of simulation steps.
+There are T such frames and the NPZ file contains the following arrays:
+
+* 'step': `(T,)` array, Md step number. 
+* 'energies': `(T,2)` array, each row containing [potential, kinetic] energies
+  in kJ/mol.
+* 'positions': `(T,num_atoms,3)` array, positions in nm.
+* 'velocities': `(T,num_atoms,3)` array, velocities in nm/ps.
+* 'forces': `(T,num_atoms,3)` array, forces in kJ/(mol nm).
+
+
+## Dataset construction
+
+The dataset was constructed in the following way:
+
+1. For the included `alanine-dipeptide.pdb` PDB file, perform a molecular
+   dynamics simulation:
+   a.) Use OpenMM with the AMBER14 force field and implicit water model.
+   b.) Perform an energy minimization (relaxation) from the initial PDB
+       configuration.
+   c.) Use a Langevin integrator at temperature T=310K, friction=0.3/ps,
+       timestep=0.5fs for 2e6 steps to equilibriate ("burn-in phase").
+   d.) Use a Langevin integrator at temperature T=310K, friction=0.3/ps,
+       timestep=0.5fs for 2e8 steps to sample a trajectory ("sample phase").
+2. Save trajectory information every 1,000 steps (0.5ps) to an `arrays.npz`
+   file.
+
+
+## Credit and Authors
+
+This dataset was created in March 2022 as part of the Molecular Simulation
+initiative.
+

AD-3/test/ad2-traj-arrays.npz

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+version https://git-lfs.github.com/spec/v1
+oid sha256:d76741027f348feebae47350ea27f06ea72db45b7635f5738f1a9dd9bac22673
+size 299733849

AD-3/test/ad2-traj-state0.pdb

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+REMARK   1 CREATED WITH OPENMM 7.7, 2022-04-23
+HETATM    1  H1  ACE A   1       2.000   1.000   0.000  1.00  0.00           H  
+HETATM    2  CH3 ACE A   1       2.000   2.090   0.000  1.00  0.00           C  
+HETATM    3  H2  ACE A   1       1.486   2.454   0.890  1.00  0.00           H  
+HETATM    4  H3  ACE A   1       1.486   2.454  -0.890  1.00  0.00           H  
+HETATM    5  C   ACE A   1       3.427   2.641   0.000  1.00  0.00           C  
+HETATM    6  O   ACE A   1       4.391   1.877   0.000  1.00  0.00           O  
+ATOM      7  N   ALA A   2       3.555   3.970   0.000  1.00  0.00           N  
+ATOM      8  H   ALA A   2       2.733   4.556   0.000  1.00  0.00           H  
+ATOM      9  CA  ALA A   2       4.853   4.614   0.000  1.00  0.00           C  
+ATOM     10  HA  ALA A   2       5.408   4.316   0.890  1.00  0.00           H  
+ATOM     11  CB  ALA A   2       5.661   4.221  -1.232  1.00  0.00           C  
+ATOM     12  HB1 ALA A   2       5.123   4.521  -2.131  1.00  0.00           H  
+ATOM     13  HB2 ALA A   2       6.630   4.719  -1.206  1.00  0.00           H  
+ATOM     14  HB3 ALA A   2       5.809   3.141  -1.241  1.00  0.00           H  
+ATOM     15  C   ALA A   2       4.713   6.129   0.000  1.00  0.00           C  
+ATOM     16  O   ALA A   2       3.601   6.653   0.000  1.00  0.00           O  
+HETATM   17  N   NME A   3       5.846   6.835   0.000  1.00  0.00           N  
+HETATM   18  H   NME A   3       6.737   6.359   0.000  1.00  0.00           H  
+HETATM   19  C   NME A   3       5.846   8.284   0.000  1.00  0.00           C  
+HETATM   20  H1  NME A   3       4.819   8.648   0.000  1.00  0.00           H  
+HETATM   21  H2  NME A   3       6.360   8.648   0.890  1.00  0.00           H  
+HETATM   22  H3  NME A   3       6.360   8.648  -0.890  1.00  0.00           H  
+TER      23      NME A   3
+CONECT    1    2    2
+CONECT    2    5    1    3
+CONECT    2    1    5    3    4
+CONECT    3    2    2
+CONECT    4    2    2
+CONECT    5    2    6    7
+CONECT    5    6    7
+CONECT    6    5    5
+CONECT    7    5    5
+CONECT   15   17   17
+CONECT   17   15   19   18
+CONECT   17   19   18
+CONECT   18   17   17
+CONECT   19   20   21   22
+CONECT   19   17   20   21   22
+CONECT   20   19   19
+CONECT   21   19   19
+CONECT   22   19   19
+END

AD-3/train/ad1-traj-arrays.npz

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+version https://git-lfs.github.com/spec/v1
+oid sha256:172187b260e3a07f24cd3eaa7528a1d1b9737526116015df5850966fa44b523c
+size 599596278

AD-3/train/ad1-traj-state0.pdb

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+REMARK   1 CREATED WITH OPENMM 7.7, 2022-04-23
+HETATM    1  H1  ACE A   1       2.000   1.000   0.000  1.00  0.00           H  
+HETATM    2  CH3 ACE A   1       2.000   2.090   0.000  1.00  0.00           C  
+HETATM    3  H2  ACE A   1       1.486   2.454   0.890  1.00  0.00           H  
+HETATM    4  H3  ACE A   1       1.486   2.454  -0.890  1.00  0.00           H  
+HETATM    5  C   ACE A   1       3.427   2.641   0.000  1.00  0.00           C  
+HETATM    6  O   ACE A   1       4.391   1.877   0.000  1.00  0.00           O  
+ATOM      7  N   ALA A   2       3.555   3.970   0.000  1.00  0.00           N  
+ATOM      8  H   ALA A   2       2.733   4.556   0.000  1.00  0.00           H  
+ATOM      9  CA  ALA A   2       4.853   4.614   0.000  1.00  0.00           C  
+ATOM     10  HA  ALA A   2       5.408   4.316   0.890  1.00  0.00           H  
+ATOM     11  CB  ALA A   2       5.661   4.221  -1.232  1.00  0.00           C  
+ATOM     12  HB1 ALA A   2       5.123   4.521  -2.131  1.00  0.00           H  
+ATOM     13  HB2 ALA A   2       6.630   4.719  -1.206  1.00  0.00           H  
+ATOM     14  HB3 ALA A   2       5.809   3.141  -1.241  1.00  0.00           H  
+ATOM     15  C   ALA A   2       4.713   6.129   0.000  1.00  0.00           C  
+ATOM     16  O   ALA A   2       3.601   6.653   0.000  1.00  0.00           O  
+HETATM   17  N   NME A   3       5.846   6.835   0.000  1.00  0.00           N  
+HETATM   18  H   NME A   3       6.737   6.359   0.000  1.00  0.00           H  
+HETATM   19  C   NME A   3       5.846   8.284   0.000  1.00  0.00           C  
+HETATM   20  H1  NME A   3       4.819   8.648   0.000  1.00  0.00           H  
+HETATM   21  H2  NME A   3       6.360   8.648   0.890  1.00  0.00           H  
+HETATM   22  H3  NME A   3       6.360   8.648  -0.890  1.00  0.00           H  
+TER      23      NME A   3
+CONECT    1    2    2
+CONECT    2    5    1    3
+CONECT    2    1    5    3    4
+CONECT    3    2    2
+CONECT    4    2    2
+CONECT    5    2    6    7
+CONECT    5    6    7
+CONECT    6    5    5
+CONECT    7    5    5
+CONECT   15   17   17
+CONECT   17   15   19   18
+CONECT   17   19   18
+CONECT   18   17   17
+CONECT   19   20   21   22
+CONECT   19   17   20   21   22
+CONECT   20   19   19
+CONECT   21   19   19
+CONECT   22   19   19
+END