Collection of scripts for the analysis of MD trajectories under Non Periodic (spherical) Boundary Conditions (NPBC)

G Mancini aug 2021

Atom / molecule selections is done using GROMACS index files. Trajectory I/O is in xtc. Dimensions are specified by each script but usually are angstroems, kJ/mol (even if internally distances are calculated in nm). A PDB topology file is needed for most calculations

dependencies

• numpy
• scipy
• mdtraj
• cython
• mendeleev

files

setup: to compile Cython functions

libraries

• npbc_io: includes functions for parsing index files, generating data for concentric layers
• npbc_analysis: includes functions to read trajectories and calculate the needed quantities frame per frame
• npbc_cy: includes some basic math/numpy based functions and Cython versions of slow analysis (e. g. ADFs)

scripts

• angular_distribution: calculate ADF for three atom groups, in given distance interval
• calc_glob: (awk script) calculate mean field VdW potential from data formatted by get_glob.awk (see DOI: 10.1021/acs.jctc.0c00454)
• continuos_hbonds: calculate HB strenght as a continuous function in [0,1] based on distance and angular cutoff (see DOI: 10.1002/jcc.24683)
• density_layer: density in concentric layers of constant radius or volume
• distance: distance between a atom group and its nth nearest neighbour from another group as a function of time
• gen_connM: (awk script) generate connectivity matrix for G16 input file for a molecule type with a central atom
• get_data_l402: parse Gaussian16 log file to extract data from a classical MDMC run in Link402 (see: 10.1021/acs.jctc.0c00454)
• get_glob: see calc_glob
• nmol: get the number of atoms/molecules within a a given distance interval from another one
• orientation: calculate the angle of a vector calculated from an atom triplet wrt to the radius of the spherical box
• pair_correlation: calculate the radial distribution function (g(r)) normalizing correctly for spherical NPBC
• pbd2com: (awk script) generate a G16 input file from a PDB and other template files
• sphere.vmd: example of selection of a sphere in VMD

notebooks

• Solvate.ipynb: example of carving a hole in a spherical box using covalent radii adjusted as in (DOI: acs.jcim.0c00076)