aggregation_md

Description and requirements

The aggregation_md project is a python script that can be used to evaluate the distribution of aggregates from molecular dynamics simulations.

The scripts are written in python 3 and require the following packages:

• MDAnalysis
• numpy
• matplotlib
• networkx
• tqdm

The script will create three directories in the current directory:

• DATA_distribution will contain the distribution of aggregates in a numpy array format
• FIGURES will contain the figures of the distribution of aggregates if the flag -pl yes is used
• check will contain a text file listing explicitly the aggregates found in the last frame of the trajectory

The directory lammps_tinker_versions contains alternatives and older scripts as the one in the main directory, but adapted to work with lammps and tinker trajectories as well as an example directory with a lammps and a tinker trajectory.

Parameters

options:
  -h, --help            show this help message and exit
  -c {yes,no}, --compute {yes,no}
                        Compute the distribution of aggregates (if no, the
                        distribution will be loaded, if it exists, in order to
                        plot it)
  -p {yes,no}, --parallel {yes,no}
                        If True, the computation will be done in parallel
  -ct CUTOFF, --cutoff CUTOFF
                        If int>1: number of frames to be skipped at the
                        beginning of the trajectory, if float<1=: proportion
                        of frames to be skipped at the beginning of the
                        trajectory
  -na N_ATOMS, --n-atoms N_ATOMS
                        Number of types of atoms considered in the analysis
  -a ATOM_TYPE [ATOM_TYPE ...], --atom_type ATOM_TYPE [ATOM_TYPE ...]
                        The type of the wanted atoms: "type A" "type B" "type
                        C", ...
  -e EPSILON [EPSILON ...], --epsilon EPSILON [EPSILON ...]
                        Distance between atoms to be considered as a pair
                        (beware of the order) : epsilon_AA, epsilon_BB, ...,
                        espilon_ZZ, epsilon_AB, epsilon_AC, ..., epsilon_YZ
  -tr TRAJ_FILE, --traj-file TRAJ_FILE
                        Trajectory file or distribution file
  -to TOP_FILE, --top-file TOP_FILE
                        Topology file
  -pl {yes,no}, --plot {yes,no}
                        Plot the distribution of aggregates
  -o OUTPUT, --output OUTPUT
                        Output file

For scripts in the subdirectory lammps_tinker_versions

Parameters

options:
  -h, --help            show this help message and exit
  -c {yes,no}, --compute {yes,no}
                        Compute the distribution of aggregates
  -p {yes,no}, --parallel {yes,no}
                        If True, the computation will be done in parallel
  -a ATOM_TYPE [ATOM_TYPE ...], --atom_type ATOM_TYPE [ATOM_TYPE ...]
                        The type of the wanted atoms: "type A" "type B" "type
                        C"
  -e EPSILON [EPSILON ...], --epsilon EPSILON [EPSILON ...]
                        Distance between atoms to be considered as a pair:
                        epsilon_AC epsilon_BC
  -tr TRAJ_FILE, --traj-file TRAJ_FILE
                        Trajectory file or distribution file
  -to TOP_FILE, --top-file TOP_FILE
                        Topology file
  -pl {yes,no}, --plot {yes,no}
                        Plot the distribution of aggregates
  -o OUTPUT, --output OUTPUT
                        Output file

Examples usage

The scripts are designed to be run from the command line. The scripts are:

• calc_distribution_1_type.py
  • Written for lammps trajectories, it looks for the aggregate made by one type of atom.
  • It can be tested using the following command:

    python3 calc_distribution_1_type.py -c yes -p yes -pl yes \
    -a "type 1" -e 2.0 -f examples/lammps/traj_1_type.lammpstrj -o distr

• calc_distribution_2_types.py
  • Written for lammps trajectories, it looks for the aggregate made by two types of atoms and three distances between them.
  • It can be tested using the following command:

    python3 calc_distribution_2_types.py -c yes -p yes -pl yes \
    -a "type 1" "type 2" -e 2.0 2.0 -f examples/lammps/traj_2_types.lammpstrj -o distr

• calc_distribution_3_types_coordination_amber.py
  • Written for amber trajectories, it looks for the coordination of an ion with organic molecules. It considers three types of atoms, but only two distances since it only considers the distance between the ion and the oxygen atom of the two possible organic molecules, forgetting about the distance between the two organic molecules, which is not relevant for the coordination.
  • It can be tested using the following command:

    python3 calc_distribution_3_types_coordination_amber.py -c yes -p yes \
    -a "resname ECA and type o" "resname PCA and type o" "resname Na+" -e 3.1 3.1 \
    -tr examples/amber/10frames.nc -to examples/amber/boite.prmtop -pl yes -o distr

• calc_distribution_3_types_coordination_tinker.py
  • This code allows to study the same kind of system as the previous one, but for simulations in tinker format.

    python3 calc_distribution_3_types_coordination_tinker.py -c yes -p no \
    -a "type 704" "type 602" "type 7" -e 3.1 3.1 \
    -tr examples/tinker/napf6_1M_in_ECDMC_2frames.arc -pl yes -o distr