Biowulf High Performance Computing at the NIH
MD-TASK: a software suite for analyzing molecular dynamics trajectories

MD-TASK is a software suite for molecular dynamics (MD). It employs graph theory techniques, perturbation response scanning, and dynamic cross-correlation to provide unique ways for analyzing MD trajectories.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=16 --mem=32g --gres=lscratch:10
[user@cn3200 ~]$module load MD-TASK 
[+] Loading gcc  9.2.0  ...
[+] Loading GSL 2.6 for GCC 9.2.0 ...
[+] Loading openmpi 4.0.5  for GCC 9.2.0
[+] Loading ImageMagick  7.0.8  on cn0848
[+] Loading HDF5  1.10.4
[+] Loading NetCDF 4.7.4_gcc9.2.0
[+] Loading pandoc  on cn0848
[+] Loading pcre2 10.21  ...
[+] Loading R 4.0.5
[+] Loading MD-TASK 1.0.0  ...
[user@cn3200 ~]$ cp $MDTASK_DATA/* .
[user@cn3200 ~]$  -h 
usage: [-h] [--topology TOPOLOGY] [--ligands LIGANDS]
                       [--threshold THRESHOLD] [--step STEP]
                       [--generate-plots] [--calc-L] [--calc-BC]
                       [--discard-graphs] [--lazy-load] [--xmgrace] [--silent]
                       [--log-file LOG_FILE]

positional arguments:
  trajectory            Trajectory file

optional arguments:
  -h, --help            show this help message and exit
  --topology TOPOLOGY   Topology PDB file (required if trajectory does not
                        contain topology information)
  --ligands LIGANDS     Specify any ligands that should be included in the
  --threshold THRESHOLD
                        Maximum distance threshold in Angstroms when
                        constructing graph (default: 6.7)
  --step STEP           Size of step when iterating through trajectory frames
  --generate-plots      Generate figures/plots
  --calc-L              Calculate delta L
  --calc-BC             Calculate delta BC
  --discard-graphs      Discard calculated networks when complete (default:
                        save networks in graphml and gml formats)
  --lazy-load           Read frames as they are needed (memory efficient - use
                        for big trajectories)
  --xmgrace             Generate xmgrace compatible format
  --silent              Turn off logging
  --log-file LOG_FILE   Output log file (default: standard output)
[user@cn3200 ~]$ --topology wt.pdb --threshold 7.0 --step 100 --generate-plots --calc-BC --calc-L --discard-graphs --lazy-load wt.dcd
INFO::Started at: 2021-06-24 10:16:59.872146
INFO::Calculating betweenness centralities...
INFO::Calculating shortest paths...
INFO::Completed at: 2021-06-24 10:17:37.774266
INFO::- Total time: 0:00:37
[user@cn3200 ~]$ -h
[user@cn3200 ~]$ -h
[user@cn3200 ~]$ -h
[user@cn3200 ~]$ -h
[user@cn3200 ~]$ -h 
[user@cn3200 ~]$ -h
[user@cn3200 ~]$ -h
[user@cn3200 ~]$ -h
End the interactive session:
[user@cn3200 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$