Unbinding Kinetics Output Files and Directories

In total, 7 folders are created corresponding to each step of the protocol:

  1. <jobname>_1-out.tgz contains the input.mae file

  2. <jobname>_2-out contains Desmond equilibration files (-out.cms) and checkpoint

  3. <jobname>_3-out.tgz contains the input (-in.cms) Desmond file that will be used for running RAMD

  4. <jobname>_4-out contains RAMD replicas. For each replica, two compressed folders are produced:

    • <jobname>_replica-01_1-out.tgz contains the -in.cms file
    • <jobname>_replica-01_3-out.tgz
      1. Reactive RAMD trajectory (.xtc and -out.cms)
      2. RAMD unbinding trajectory descriptors (trj_descriptors.png)
      3. The unbinding path (path.mae)

    The folder also contains a checkpoint and log file for every replica. In the log file (e.g. <jobname>_replica-01_multisim.log), the mean RAMD time and SD are reported.

  5. <jobname>_5-out.tgz contains the unbinding pathway clustering results. In particular:

    • ramd_unbinding_path_summary.maegz shows all the unbinding pathways, from all the replicas, grouped into clusters
    • <jobname>_cluster0.maegz contains the most representative unbinding pathway that will be used as reaction coordinate during Infrequent Metadynamics
    • Input (.cms) Desmond file for running Infrequent Metadynamics

  6. <jobname>_6-out contains Metadynamics replicas. For all replicas, the following files are generated:

    • Multisim log file
    • <jobname>_mtd_replica-C-XX_3-out.tgz folder which contains Metadynamics "parched" trajectories (.xtc and -out.cms)
    • Checkpoint file for restarting the subjob.

  7. <jobname>_7-out contains data summarizing final predictions. There is both a zipped and unzipped version. The zipped file has additional content. The contents of these files are:

    • A .dat file with a summary of the results and residence time prediction.
    • A PNG image file containing the residence time prediction and fitting to cumulative distribution function (CDF) related statistical parameters
    • PNG images showing the path CV trajectories for each replica (in .tgz)
    • Structures from the simulation summarizing the sampling along the path (in .tgz)