- Center of mass vector
- Calculate the vector between the centers of mass of
s1
and s2
- The vector is calculated as
s1
- s2
- The following example generates features about COM vector for MSM analysis
pacs genfeature comvec mdtraj -t 1 -tf prd.xtc -top inputs/input.gro -ref inputs/input.gro -ft "name CA" -fr "name CA" -s1 "resid 1" -s2 "resid 9"
usage: pacs genfeature comvec mdtraj [-h] [-t] [-tf] [-top] [-od] [-p] [-ref] [-ft] [-fr] [-s1] [-s2]
-t, --trial
(int):
- trial number without 0-fill
-tf, --trj-file
(str):
- trajectory file name (e.g. prd.xtc prd_rmmol.trr)
-top, --topology
(str):
- topology file path (e.g. .inputs/input.gro)
-od, --outdir
(str):
-p, --n_parallel
(int):
-ref, --reference
(str):
- reference file path for fitting
-ft, --fit-trj
(str):
- fitting selection for mdtraj in trajectory
-fr, --fit-ref
(str):
- fitting selection for mdtraj in reference
-s1, --selection1
(str):
- mdtraj selection1 for calculating distance
-s2, --selection1
(str):
- mdtraj selection2 for calculating distance