MDTransport

MDTransport: Python Tool for Computing Transport Properties from GROMACS and LAMMPS Simulations

MDTransport is a powerful and flexible command-line tool designed to streamline the analysis of transport properties from Molecular Dynamics (MD) simulations. It provides a unified interface for post-processing trajectory data from both GROMACS and LAMMPS.

Installation Guide

Prerequisites

The following base dependencies are required:

python >= 3.9
matplotlib >= 3.6
pandas >= 2.0
numpy >= 1.20
scipy >= 1.10
tqdm >= 4.60

Optional Dependencies

Depending on the specific engine you wish to use for trajectory parsing, you may need one of the following:

Click to view optional installations (MDAnalysis, Chemfiles, Ovito)

MDAnalysis (Required for --mda option)

conda install -c conda-forge mdanalysis

or

pip install MDAnalysis
Chemfiles (Required for --chem option)

conda install -c conda-forge chemfiles

or

pip install chemfiles
Ovito (Required for --ovito option)

conda install -c conda-forge ovito

or

pip install ovito

Installation via Package Managers

MDTransport is available as a pre-compiled package for Linux, macOS, and Windows.

Via PyPI:

pip install MDTransport

Via Conda-forge:

conda install -c conda-forge mdtransport

Build From Sources

You can install the latest development version directly from GitHub:

git clone https://github.com/ShahResearchGroup/MDTransport.git

cd MDTransport

Using pip

pip install -e .

OR using a Conda environment

conda env create -f environment.yml conda activate mdt_env chmod +x mdt.py

Argument Flags

General Analysis Modes

Flag	Description
`--gro`	Run GROMACS analysis.
`--lam`	Run LAMMPS analysis.

Trajectory Parsing Modes

Flag	Engine	Description & Example
`--pdb`	GROMACS	Use PDB file to extract species data.
`--exe`	GROMACS	Use gmx to extract species data (e.g., `--exe gmx` or `--exe gmx_mpi`).
`--lamp`	LAMMPS	Use lammpstrj file to extract species data.
`--com`	LAMMPS	Use LAMMPS generated com.txt (e.g., `--com /path/to/com.txt`).
`--chem`	Both	Use Chemfiles to extract species data.
`--mda`	Both	Use MDAnalysis to extract species data.
`--ovito`	Both	Use Ovito to extract species data.

File & Path Arguments

Flag	Description	Example
`--in`	Path to MDTransport input file	`--in /path/to/input`
`--itp`	Directory containing GROMACS ITP files	`--itp /path/to/itp/`
`--tpr`	Path to GROMACS TPR file	`--tpr /path/to/file.tpr`
`--traj`	Path to trajectory file	`--traj /path/to/file.trr`
`--data`	Path to LAMMPS data file	`--data /path/to/data`
`--lam_in`	Path to LAMMPS input file	`--lam_in /path/to/input`
`--gro_path`	Path to GROMACS files directory	`--gro_path /path/to/gromacs/`
`--lam_path`	Path to LAMMPS files directory	`--lam_path /path/to/lammps/`

General Parameters

Flag	Description	Example
`--temp`	Temperature in Kelvin	`--temp 298.0`
`--t_steps`	Time steps in ps	`--t_steps 2`
`--n_delta`	Time window for time origins shifting in ps	`--n_delta 1000`
`--t_window`	Time window for slope calculations in ps	`--t_window 1000`
`--min_window`	Minimum time window for diffusivity calculations in ps	`--min_window 1000`
`--n_steps`	Snapshots range in frames	`--n_steps 0 20000`
`--fit_method`	MSD fitting method for diffusion calculations	`--fit_method gls`
`--msd_fit`	Time window (in ps) for MSD fitting: start end	`--msd_fit 10000 40000`
`--steps`	Steps for time origin shifting	`--steps 20`
`--dir`	Specify directions for msd/diffusion	`--dir x y z`
`--n`	Process every N-th frame	`--n 5`
`--dump_frame`	LAMMPS trajectory dumping frame	`--dump_frame 1000`
`--n_cores`	Number of CPU cores for parallel processing	`--n_cores 8`
`--mp_mode`	Multi-processing initialization	`--mp_mode fork`

Properties Calculations

Flag	Description
`--msd`	Compute mean squared displacement and diffusion.
`--corr`	Calculate ion-ion correlations and Einstein conductivity.
`--onsg`	Calculate Onsager transport coefficients.
`--spda`	Spatial decomposition of ion-ion correlations.
`--en`	Calculate Einstein conductivity.
`--ne`	Calculate Nernst-Einstein conductivity.
`--smd`	Run Stefan-Maxwell diffusivity analysis.
`--pcl`	Calculate pair correlation lifetime.
`--cage_p`	Cage population analysis.
`--cage`	Calculate cage correlation lifetime.
`--veh`	Run transport mechanism analysis.
`--rdf`	Calculate radial distribution functions.
`--get_csv`	Parse and save trajectories data.

Analysis-Specific Parameters

Flag	Description	Example
`--species`	Define species names and counts for LAMMPS	`--species EMI 500 BF4 500`
`--resname`	Define species names	`--resname EMI BF`
`--skip_species`	Exclude Resnames from COM generation	`--skip_species SOL`
`--rcut`	Cutoff radius for analysis	`--rcut 7.6`
`--rbin`	RDF bin size	`--rbin 0.2`
`--ref_species`	Reference species for cage correlation	`--ref_species EMI`
`--cage_species`	Cage species for cage correlation	`--cage_species BF`
`--ana`	Run optional RDFs analysis	`--ana`
`--eh`	Enable Einstein-Helfand for TRA and ONSG analysis	`--eh`
`--rdf_mode`	Specify the RDF calculation mode	`--rdf_mode com com`
`--rdf_pairs`	Specify the RDF pairs	`--rdf_pairs resname EMI type HR resname BF type F`
`--msd_mode`	Specify the MSD calculation mode	`--msd_mode com`
`--msd_species`	Specify the MSD species	`--msd_species type 1-6 type 7-12`
`--shell`	Solvation shell choice for SPDA	`--shell first`
`--species_charges`	Override net charges on each species	`--species_charges EMI 0.8`

Commands Usage

Note: [MODE] in the examples below refers to your chosen file parsing backend:

GROMACS Modes: --pdb --traj <pdb file> --itp <itp directory> OR --exe <gmx> OR --mda OR --chem OR --ovito

LAMMPS Modes: --lamp OR --com <com file> OR --mda OR --chem OR --ovito

1. MSD and Diffusion Analysis

COM-based MSD for Species

GROMACS:

mdt --gro --msd [MODE] --t_steps <time steps> --skip_species <resname> --dir <x, y, z> --n_steps <start frame> <end frame> --min_window <min. time window>

LAMMPS:

mdt --lam --msd [MODE] --t_steps <time steps> --dir <x, y, z> --n <frame stride> --dump_frame <steps> --min_window <min. time window> --n_steps <start frame> <end frame>

COM-based MSD for Selected Groups

GROMACS:

mdt --gro --msd [MODE] --t_steps <time steps> --min_window <min. time window> --dir <x, y, z> --msd_mode com --msd_species resname <resname> type <atom type> <atom type> --n_steps <start frame> <end frame>

LAMMPS:

mdt --lam --msd [MODE] --dump_frame <steps> --t_steps <time steps> --n <frame stride> --dir <x, y, z> --n_steps <start frame> <end frame> --min_window <min. time window> --msd_mode com --msd_species resname <resname> type 1 2

Atom-based MSD for Selected Atoms

GROMACS:

mdt --gro --msd [MODE] --t_steps <time steps> --min_window <min. time window> --dir <x, y, z> --msd_mode atom --msd_species resname <resname> type <atom type> --n_steps <start frame> <end frame>

LAMMPS:

mdt --lam --msd [MODE] --dump_frame <steps> --t_steps <time steps> --n <frame stride> --dir <x, y, z> --n_steps <start frame> <end frame> --min_window <min. time window> --msd_mode atom --msd_species resname <resname> type <atom type>

2. Conductivity & Transport Analysis

Nernst-Einstein Conductivity (`--ne`)

GROMACS:

mdt --gro --ne [MODE] --t_steps <time steps> --skip_species <resname> --temp <temperature> --n_steps <start frame> <end frame> --min_window <min. time window>

LAMMPS:

mdt --lam --ne [MODE] --t_steps <time steps> --dump_frame <steps> --n <frame stride> --temp <temperature> --n_steps <start frame> <end frame> --min_window <min. time window>

Einstein Conductivity Using Einstein-Helfand (`--en`)

GROMACS:

mdt --gro --en [MODE] --t_steps <time steps> --t_window <time window for slope> --n_steps <start frame> <end frame> --temp <temperature>

LAMMPS:

mdt --lam --en [MODE] --t_steps <time steps> --dump_frame <steps> --t_window <time window for slope> --n <frame stride> --n_steps <start frame> <end frame> --temp <temperature>

Onsager Transport Coefficients (`--onsg`)

GROMACS:

mdt --gro --onsg [MODE] --t_steps <time steps> --t_window <time window for slope> --temp <temperature> --n_steps <start frame> <end frame> --n_delta <window>

LAMMPS:

mdt --lam --onsg [MODE] --t_steps <time steps> --dump_frame <steps> --temp <temperature> --n <frame stride> --t_window <time window for slope> --n_steps <start frame> <end frame> --n_delta <window>

Ionic Conductivity Using Stefan-Maxwell Diffusivity (`--smd`)

GROMACS:

mdt --gro --smd [MODE] --t_steps <time steps> --temp <temperature> --n_steps <start frame> <end frame> --min_window <min. time window>

LAMMPS:

mdt --lam --smd [MODE] --t_steps <time steps> --dump_frame <steps> --n <frame stride> --temp <temperature> --n_steps <start frame> <end frame> --min_window <min. time window>

Transport Mechanism of Species (`--veh`)

GROMACS:

mdt --gro --veh [MODE] --t_steps <time steps> --min_window <min. time window> --rcut <first solvation> --temp <temperature> --steps <time origin steps> --n_steps <start frame> <end frame> --resname <reference species> <target species>

LAMMPS:

mdt --lam --veh [MODE] --t_steps <time steps> --dump_frame <steps> --min_window <min. time window> --n <frame stride> --n_steps <start> <end> --temp <temperature> --rcut <first solvation> --steps <time origin steps> --resname <reference species> <target species>

3. Correlations & Structure

Ion-Ion Correlations (`--corr`)

GROMACS:

mdt --gro --corr [MODE] --t_steps <time steps> --n_delta <window for time origin shifting> --temp <temperature> --n_steps <start frame> <end frame> --t_window <time window for slope>

LAMMPS:

mdt --lam --corr [MODE] --t_steps <time steps> --dump_frame <steps> --n_delta <window for time origin shifting> --n <frame stride> --n_steps <start frame> <end frame> --temp <temperature> --t_window <time window>

Spatial Decomposition Analysis of Ion-Ion Correlations (`--spda`)

GROMACS:

mdt --gro --spda [MODE] --t_steps <time steps> --n_delta <window for time origin shifting> --temp <temperature> --n_steps <start frame> <end frame> --t_window <time window for slope>

LAMMPS:

mdt --lam --spda [MODE] --t_steps <time steps> --dump_frame <steps> --n_delta <window for time origin shifting> --n <frame stride> --n_steps <start frame> <end frame> --temp <temperature> --t_window <time window>

Radial Distribution Function Calculation (`--rdf`)

COM-COM RDF:

GROMACS

mdt --gro --rdf [MODE] --t_steps <time steps> --n_steps <start> <end> --steps <time origins> mdt --gro --rdf [MODE] --rdf_mode com com --rdf_pairs resname <res> type <type> <type> resname <res> type <type> <type>

LAMMPS

mdt --lam --rdf [MODE] --n <frame stride> --t_steps <time steps> --n_steps <start> <end> --dump_frame <steps> mdt --lam --rdf [MODE] --rdf_mode com com --rdf_pairs resname <res> type <type> <type> resname <res> type <type> <type>

ATOM-COM RDF:

GROMACS

mdt --gro --rdf [MODE] --rdf_mode atom com --rdf_pairs resname <res> type <type> resname <res> type <type> <type>

LAMMPS

mdt --lam --rdf [MODE] --rdf_mode atom com --rdf_pairs resname <res> type <type> resname <res> type <type> <type>

ATOM-ATOM RDF:

GROMACS

mdt --gro --rdf [MODE] --rdf_mode atom atom --rdf_pairs resname <res> type <type> resname <res> type <type>

LAMMPS

mdt --lam --rdf [MODE] --rdf_mode atom atom --rdf_pairs resname <res> type <type> resname <res> type <type>

Cluster Analysis (`--cage_p`)

GROMACS:

mdt --gro --cage_p [MODE] --t_steps <time steps> --n_steps <start frame> <end frame> --rcut <first solvation> --resname <reference species> <target species>

LAMMPS:

mdt --lam --cage_p [MODE] --n <frame stride> --dump_frame <steps> --species <resname> <numbers> --rcut <first solvation> --n_steps <start frame> <end frame> --t_steps <time steps> --resname <reference species> <target species>

Cage Correlation Lifetime (`--cage`)

GROMACS:

mdt --gro --cage [MODE] --ref_species <resname> --cage_species <resname> --n_steps <start frame> <end frame> --t_steps <time steps> --rcut <first solvation> --steps <time origin steps>

LAMMPS:

mdt --lam --cage [MODE] --t_steps <time steps> --dump_frame <steps> --ref_species <resname> --cage_species <resname> --n_steps <start frame> <end frame> --rcut <first solvation> --steps <time origin steps> --n <frame stride>

Pair Correlation Lifetime (`--pcl`)

GROMACS:

mdt --gro --pcl [MODE] --t_steps <time steps> --n_steps <start frame> <end frame> --steps <time origin steps> --resname <reference species> <target species>

LAMMPS:

`mdt --lam --pcl [MODE] --dump_frame --t_steps --species --n --n_steps --steps --resname '

Citation

If you use MDTransport for your research, please cite: Ashutosh Verma, Amey S. Thorat, and Jindal K. Shah, "MDTransport: A Modular, Open-Source, Extensible Python Tool for Computing Transport Properties from GROMACS and LAMMPS Simulations." Journal of Chemical Information and Modeling, 2026, https://doi.org/10.1021/acs.jcim.6c00558

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README.md		README.md
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mdt.py		mdt.py
pyproject.toml		pyproject.toml

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MDTransport

Table of Contents

Installation Guide

Prerequisites

Optional Dependencies

or

or

or

Installation via Package Managers

Build From Sources

Using pip

OR using a Conda environment

Argument Flags

General Analysis Modes

Trajectory Parsing Modes

File & Path Arguments

General Parameters

Properties Calculations

Analysis-Specific Parameters

Commands Usage

1. MSD and Diffusion Analysis

COM-based MSD for Species

COM-based MSD for Selected Groups

Atom-based MSD for Selected Atoms

2. Conductivity & Transport Analysis

Nernst-Einstein Conductivity (--ne)

Einstein Conductivity Using Einstein-Helfand (--en)

Onsager Transport Coefficients (--onsg)

Ionic Conductivity Using Stefan-Maxwell Diffusivity (--smd)

Transport Mechanism of Species (--veh)

3. Correlations & Structure

Ion-Ion Correlations (--corr)

Spatial Decomposition Analysis of Ion-Ion Correlations (--spda)

Radial Distribution Function Calculation (--rdf)

GROMACS

LAMMPS

GROMACS

LAMMPS

GROMACS

LAMMPS

Cluster Analysis (--cage_p)

Cage Correlation Lifetime (--cage)

Pair Correlation Lifetime (--pcl)

Citation

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Nernst-Einstein Conductivity (`--ne`)

Einstein Conductivity Using Einstein-Helfand (`--en`)

Onsager Transport Coefficients (`--onsg`)

Ionic Conductivity Using Stefan-Maxwell Diffusivity (`--smd`)

Transport Mechanism of Species (`--veh`)

Ion-Ion Correlations (`--corr`)

Spatial Decomposition Analysis of Ion-Ion Correlations (`--spda`)

Radial Distribution Function Calculation (`--rdf`)

Cluster Analysis (`--cage_p`)

Cage Correlation Lifetime (`--cage`)

Pair Correlation Lifetime (`--pcl`)