OpenMMDL Simulation Output Files

The OpenMMDL Simulation script creates output folders and files during and after the simulation.

The following list contains a detailed overview of the folders and files: Optional files are highlighted with an asterisk.

Input Files

Input Files: A folder that contains the PDB and SDF files, which served as input files for the MD simulation.

Name	Description
Protein_name.pdb*	Protein PDB file that served as the input for the MD simulation.
ligand_name.sdf*	Ligand SDF file that served as the input for the MD simulation.
ligand_name.mol / ligand_name.mol2*	Additional ligand or cofactor files that served as input for the MD simulation.
ligand_*_pc.mol2*	Ligand MOL2 files written with partial charges for downstream analysis and inspection.

Checkpoints

Checkpoints: A folder that contains checkpoints, which can be used to restart the MD Simulation.

Name	Description
checkpoint.chk	Checkpoint saved every 10000 steps.
10x_checkpoint.chk	Checkpoint saved every 100000 steps.
100x_checkpoint.chk*	Checkpoint saved every 1000000 steps.

MD Files

MD Files: A folder that contains the files that were generated during the MD simulation. This folder contains 3 subfolders.

Pre MD: Folder that contains the files that were prepared by the script before the MD simulation.

Name	Description
prepared_no_solvent_protein_name.pdb	Prepared PDB file without solvent or membrane.
solvent_padding_protein_name.pdb*	Prepared PDB file with padding solvent.
solvent_absolute_protein_name.pdb*	Prepared PDB file with absolute solvent.
membrane_protein_name.pdb*	Prepared PDB file with membrane.

Minimization Equilibration: Folder that contains topology files after the minimization and equilibration with OpenMM.

Name	Description
Energyminimization_protein_name.pdb	Prepared PDB file after OpenMM energy minimization.
Equilibration_protein_name.pdb	Prepared PDB file after OpenMM energy minimization and equilibration.

MD Output: Folder that contains the output trajectory files generated during the MD simulation.

Name	Description
output_protein_name.pdb	PDB topology file of the first frame of the simulation.
trajectory.dcd	Trajectory of the OpenMM Simulation.

MD Postprocessing

MD Postprocessing: A folder that contains the postprocessing files after the MD simulation.

Name	Description
centered_old_coordinates_top.pdb	Topology file of the centered protein in PDB format.
centered_old_coordinates_top.gro	Topology file of the centered protein in Gromacs GRO format.
centered_old_coordinates.dcd	Trajectory file of the centered protein in DCD format.
centered_old_coordinates.xtc	Trajectory file of the centered protein in XTC format.
centered_traj_unaligned.dcd	Trajectory file of the unaligned centered protein in DCD format with all atoms and new coordinates.
centered_traj_unaligned.xtc	Trajectory file of the unaligned centered protein in XTC format with all atoms and new coordinates.
prot_lig_traj_unaligned.dcd*	Trajectory file of the unaligned centered protein in DCD format with only protein and ligand atoms and new coordinates.
prot_lig_traj_unaligned.xtc*	Trajectory file of the unaligned centered protein in XTC format with only protein and ligand atoms and new coordinates.

Final Output

Final Output: A folder that contains the final files after the MD simulation, ready to be analyzed. Depending on the selected MDAnalysis output mode, this folder may contain All_Atoms, Prot_Lig, or both subfolders.

1. All Atoms: Folder that contains the centered topology files of all atoms with new coordinates according to the center of mass.

Name	Description
centered_top.pdb*	Topology file of the centered protein in PDB format with all atoms and new coordinates.
centered_top.gro*	Topology file of the centered protein in Gromacs GRO format with all atoms and new coordinates.
centered_traj.dcd*	Trajectory file of the aligned centered protein in DCD format with all atoms and new coordinates.
centered_traj.xtc*	Trajectory file of the aligned centered protein in XTC format with all atoms and new coordinates.
ligand_name.sdf / ligand_name.mol / ligand_name.mol2*	Ligand and cofactor input files copied into the final all-atoms output folder.
ligand_*_pc.mol2*	Ligand MOL2 files with partial charges copied into the final all-atoms output folder.

2. Prot Lig: Folder that contains the centered topology files of only the protein and ligand atoms with new coordinates according to the center of mass.

Name	Description
prot_lig_top.pdb*	Topology file of the centered protein in PDB format with only protein and ligand atoms and new coordinates.
prot_lig_top.gro*	Topology file of the centered protein in Gromacs GRO format with only protein and ligand atoms and new coordinates.
prot_lig_traj.dcd*	Trajectory file of the centered protein in DCD format with only protein and ligand atoms and new coordinates.
prot_lig_traj.xtc*	Trajectory file of the centered protein in XTC format with only protein and ligand atoms and new coordinates.
ligand_name.sdf / ligand_name.mol / ligand_name.mol2*	Ligand and cofactor input files copied into the final protein-ligand output folder.
ligand_*_pc.mol2*	Ligand MOL2 files with partial charges copied into the final protein-ligand output folder.