cgib

  • For more details about the options --top and --name, see here.

  • For more details about the option --traj, see here.

  • The option --exclude excludes 1-2, 1-3, 1-4 neighbors when building the pair-list. It takes a string with 3 bits, each bit is 1 or 0 switching the types of neighbors on or off. Deafult “111” means excluding all bonding neighbors.

  • The script generates a list of result files for each targeted variable specified in the options. The files are named as [Pair/Bond/Angle/Dihedral]-[Types].dat. The result file contains three columns: the variable, the relative probability density, and the IB potential.

  • The options --pair, --bond, and --angle are used to do histogram analysis for centain pair-types, bond-types, and angle-types. The multi-field values always comes with a number of type names (two for pair and bond, and three for angle), and are followed by the arguments for the histogram: min-value, max-value, and number of bins.

  • If the option --plot is specified, the script will visualize the result by using the Python matplotlib package.

Notes

  • For the distribution of pair distances, the results have been normalized by the volume-correction factor, \((4 \pi r^2)^{-1}\), and by average particle density probability so that the curve approach 1. These results corespond to the radial distribution function (RDF).

  • For other distributions (bonds, angles and dihedral torsions), results are scaled to give a maximum value of 1. So, the numbers can be intepreted as the relative probability to the most probable value.

  • If you have used the old MSCGFM software, this command is a replacement to the rangerfinder.

Examples

cgib --top tests/data/methanol_1728.data \
     --traj tests/data/methanol_1728_cg.trr \
     --names MeOH --cut 10.0 --temp 298.15 \
     --pair MeOH,MeOH,min=2.4,max=10.0,bins=200

cgib --top tests/data/methanol_1728_2s.data \
     --traj tests/data/methanol_1728_2s.trr \
     --names CH3,OH --cut 10.0 --temp 298.15 \
     --pair CH3,CH3,min=2.4,max=10.0,bins=200 \
     --pair CH3,OH,min=2.4,max=10.0,bins=200 \
     --pair OH,OH,min=2.0,max=10.0,bins=200 \
     --bond CH3,OH,min=1.35,max=1.65,bins=60 \
     --plot n