**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. .. list-table:: :header-rows: 1 :widths: 25 75 * - 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. .. list-table:: :header-rows: 1 :widths: 25 75 * - 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. .. list-table:: :header-rows: 1 :widths: 25 75 * - 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**. .. list-table:: :header-rows: 1 :widths: 25 75 * - 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. .. list-table:: :header-rows: 1 :widths: 25 75 * - 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. .. list-table:: :header-rows: 1 :widths: 25 75 * - 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. .. list-table:: :header-rows: 1 :widths: 25 75 * - 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. .. list-table:: :header-rows: 1 :widths: 25 75 * - 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.