1.2 Pairwise Interaction energies (PWIE)

Calculating Pairwise residue interaction energies

dyno_pwie.py uses cpptraj from ambertools to calculate the residue pairwise interaction energies. From the pair range (-f FIRST RESIDUE -l LAST RESIDUE) it generates the list of pairs, divides them into sets of size -p 8 (max 15) and runs -n instances of cpptraj in parallel. Per residue pair (i,j), will generate IE-i-j-LABEL.h5 compressed files with two columns of data i.e. van Der Waals and electrostatic interaction energies.

input options:

  -x TRJ, --trj TRJ     trajectory file <xtc/binpos/netcdf> any format cpptraj can process
  -t TOP, --top TOP     topology file
  -f FST, --fst FST     first residue
  -l LST, --lst LST     last residue
  -p PMAX, --pmax PMAX  maximum number of pairs per cpptraj instance
  -n TMAX, --tmax TMAX  number of threads to use each thread will run one cpptraj instance. Depending on the trajectory size and available free RAM, change this option. Do not use more than 50% of the available threads.
  -o LABEL, --label LABEL Label to add to all the files

sample usage:

dyno_pwie.py -x trajectory -t topology -f 1 -l 200 -p 10 -n 8 -o LABEL