cgderiv

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

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

  • For more details about the option for models, such as --pair, --bond, --angle or --dihedral, 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.

Notes

  • The output of this script will be stored in a Python Pickle file, which can be opened and read by standard Python libraries. The data inside the Pickle file is a dictionary with three keys:

    • models: serialized model definitions.

    • dudl_mean: ensemble averages of the potential energy parameterization derivatives from each model stored as a dictionary indexed by the model name. The value of corresponding to each model is a Numpy array.

    • dudl_var: similar to dudl_mean, but the contents are the variances of the derivatives.

Examples

cgderiv --top water_512_cg.data \
        --traj water_512_cg.lammpstrj \
        --names SL --cut 7.0 \
        --pair model=BSpline,type=SL:SL,min=2.4,max=7.0,resolution=0.2,order=4