MDTransport Terminal
1. Parser
2. Files
3. Analysis
4. Parameters
5. Advanced
MDTransport: Python Tool for Computing Transport Properties from GROMACS and LAMMPS Simulations
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Limitations:
- Advanced libraries like MDAnalysis, Chemfiles, and Ovito are not available
- Best suited for standard GROMACS *.pdb and LAMMPS *.lammpstrj files
- Advanced libraries like MDAnalysis, Chemfiles, and Ovito are not available
- Best suited for standard GROMACS *.pdb and LAMMPS *.lammpstrj files
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Linux
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Installation Guide
Argument Flags
Commands Usage
The following dependencies are required:
python >=3.9
matplotlib >=3.6
pandas >=2.0
numpy >=1.20
scipy >=1.10
tqdm >=4.60MDAnalysis Requirements
MDAnalysis is required only if you intend to use the --mda option.
Installation options:
# Recommended if using Conda
conda install -c conda-forge mdanalysis
# Alternative using pip
pip install MDAnalysisChemfiles Requirements
Chemfiles is required only if you intend to use the --chem option.
Installation options:
# Recommended if using Conda (Anaconda/Miniconda)
conda install -c conda-forge chemfiles
# Alternative using pip
pip install chemfilesOvito Requirements
Ovito is required only if you intend to use the --ovito option.
Installation options:
# Recommended if using Conda (Anaconda/Miniconda)
conda install -c conda-forge ovito
# Alternative using pip
pip install ovitoCreate a Virtual Environment and Run MDTransport Directly
git clone https://github.com/ShahResearchGroup/MDTransport.git
cd MDTransport
conda env create -f environment.yml
conda activate mdt_env
chmod +x mdt.pyBuild From Sources
MDTransport is available on GitHub page and can be install using pip
pip install git+https://github.com/ShahResearchGroup/MDTransport.git
or
git clone https://github.com/ShahResearchGroup/MDTransport.git
cd MDTransport
pip install -e .Installation via Package Managers
MDTransport is available as a pre-compiled package for Linux, macOS, and Windows. It can be installed through the Python Package Index (PyPI) or the Conda-forge channel.
To install the package via PyPI, use:
pip install MDTransportAlternatively, MDTransport can be installed via Conda-forge:
conda install -c conda-forge mdtransportGeneral Analysis Modes
[--gro] : Run GROMACS analysis.
[--lam] : Run LAMMPS analysis.GROMACS Analysis Modes
[--pdb] : Use PDB file to extract species data (e.g., --pdb).
[--exe] : Use gmx to extract species data from GROMACS files (e.g., --exe gmx).
[--chem] : Use Chemfiles to extract species data from GROMACS files (e.g., --chem).
[--mda] : Use MDAnalysis to extract species data from GROMACS files (e.g., --mda).
[--ovito] : Use Ovito to extract species data from GROMACS files (e.g., --ovito).LAMMPS Analysis Modes
[--lamp] : Use lammpstrj file to extract species data (e.g., --lamp).
[--com] : Use LAMMPS generated com.txt to extract species data (e.g., --com /path/to/com/file).
[--chem] : Use Chemfiles to extract species data from LAMMPS files (e.g., --chem).
[--mda] : Use MDAnalysis to extract species data from LAMMPS files (e.g., --mda).
[--ovito] : Use Ovito to extract species data from LAMMPS files (e.g., --ovito).File & Path Arguments
[--in] : Path to MDTransport input file (e.g., --in /path/to/input/file).
[--itp] : Directory containing GROMACS ITP files (e.g., --itp /path/to/itp/directory).
[--tpr] : Path to GROMACS TPR file (e.g., --tpr /path/to/tpr/file).
[--traj] : Path to trajectory file (e.g., --traj /path/to/trajectory/file).
[--data] : Path to LAMMPS data file (e.g., --data /path/to/data/file).
[--lam_in] : Path to LAMMPS input file (e.g., --lam_in /path/to/input/file).
[--gro_path] : Path to GROMACS files directory (e.g., --gro_path /path/to/gromacs/files).
[--lam_path] : Path to LAMMPS files directory (e.g., --lam_path /path/to/lammps/files).General Parameters
[--temp] : Temperature in Kelvin (e.g., --temp 298.0).
[--t_steps] : Time steps in ps (e.g., --t_steps 2).
[--n_delta] : Time window for time origins shifting in ps (e.g., --n_delta 1000).
[--t_window] : Time window for slope calculations in ps (e.g., --t_window 1000).
[--min_window] : Minimum time window for diffusivity calculations in ps (e.g., --min_window 1000).
[--n_steps] : Snapshots range in ps (e.g., --n_steps 0 20000).
[--fit_method] : MSD fitting method for diffusion calculations (e.g., --fit_method gls).
[--msd_fit] : MSD fitting window in ps (e.g., --msd_fit 10000 40000).
[--steps] : Steps for time origin shifting (e.g., --steps 20).
[--dir] : Specify directions for msd/diffusion (e.g., --dir x y z).
[--n] : process every N-th frame (e.g., --n 5).
[--dump_frame] : LAMMPS trajectory dumping frame (e.g., --dump_frame 1000).
[--n_cores] : Number of CPU cores to use for parallel processing (e.g., --n_cores 8).
[--mp_mode] : Multi-processing initialization (e.g., --mp_mode fork).Properties Calculations
[--msd] : Compute mean squared displacement and diffusion (e.g., --msd).
[--corr] : Calculate ion-ion correlations and Einstein conductivity (e.g., --corr).
[--onsg] : Calculate Onsager transport coefficients (e.g., --onsg).
[--spda] : Spatial decomposition of ion-ion correlations (e.g., --spda).
[--en] : Calculate Einstein conductivity (e.g., --en).
[--ne] : Calculate Nernst-Einstein conductivity (e.g., --ne).
[--smd] : Run Stefan-Maxwell diffusivity analysis (e.g., --smd).
[--pcl] : Calculate pair correlation lifetime (e.g., --pcl).
[--cage_p] : Cage population analysis (e.g., --cage_p).
[--cage] : Calculate cage correlation lifetime (e.g., --cage).
[--veh] : Run transport mechanism analysis (e.g., --veh).
[--rdf] : Calculate radial distribution functions (e.g., --rdf).
[--get_csv] : Parse and save trajectories data. (e.g., --get_csv).Analysis-Specific Parameters
[--species] : Define species names and counts for LAMMPS (e.g., --species EMI 500 BF4 500)
[--resname] : Define species names (e.g., --resname EMI BF)
[--skip_species] : Exclude Resnames from COM generation (e.g., --skip_species SOL).
[--rcut] : Cutoff radius for analysis (e.g., --rcut 7.6).
[--rbin] : RDF bin size (e.g., --rbin 0.2)
[--ref_species] : Reference species for cage correlation (e.g., --ref_species EMI).
[--cage_species] : Cage species for cage correlation (e.g., --cage_species BF).
[--ana] : Run optional RDFs analysis (e.g., --ana).
[--eh] : Enable Einstein-Helfand for TRA and ONSG analysis (e.g., --eh).
[--rdf_mode] : Specify the RDF calculation mode (e.g., --rdf_mode com com)
[--rdf_pairs] : Specify the RDF pairs.
(e.g., --rdf_pairs resname EMI type HR resname BF type F)
(e.g., --rdf_pairs type 1-6 type 7-12)
[--msd_mode] : Specify the MSD calculation mode (e.g., --msd_mode com)
[--msd_species] : Specify the MSD species.
(e.g., --msd_species resname EMI type HR resname BF type F)
(e.g., --msd_species type 1-6 type 7-12)
[--shell] : Solvation shell choice for SPDA (e.g., --shell first).
[--species_charges] : Override net charges on each species (e.g., --species_charges 1 or --species_charges EMI 0.8).Common GROMACS parsers
[Parser] :[--pdb / --exe / --mda / --chem / --ovito] Common LAMMPS parsers
[Parser] :[--lamp / --com / --mda / --chem / --ovito] MSD and Diffusion Analysis
COM-based MSD for Species
GROMACSmdt [--gro] [--msd] [Parser]
[--t_steps <time steps>] [--skip_species <resname>] [--dir <x, y, z>]
[--n_steps <start frame> <end frame>] [--min_window <min. time window>]mdt [--lam] [--msd] [Parser]
[--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
GROMACSmdt [--gro] [--msd] [Parser]
[--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>]
mdt [--gro] [--msd] [Parser]
[--t_steps <time steps>] [--min_window <min. time window>] [--dir <x, y, z>]
[--msd_mode com --msd_species resname <resname> name <atom name> <atom name>]
[--n_steps <start frame> <end frame>]
mdt [--gro] [--msd] [Parser]
[--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>
resname <resname> type <atom type> <atom type>] [--n_steps <start frame> <end frame>]
mdt [--gro] [--msd] [Parser]
[--t_steps <time steps>] [--min_window <min. time window>] [--dir <x, y, z>]
[--msd_mode com --msd_species resname <resname> name <atom name> <atom name>
resname <resname> name <atom name> <atom name>] [--n_steps <start frame> <end frame>]mdt [--lam] [--msd] [Parser]
[--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]
mdt [--lam] [--msd] [Parser]
[--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 <atom type> <atom type> resname <resname>]
mdt [--lam] [--msd] [Parser]
[--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 <atom type> <atom type>
resname <resname> type <atom type> <atom type>]
mdt [--lam] [--msd] [Parser]
[--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> resname <resname>]Atom-based MSD for Selected Atoms
GROMACSmdt [--gro] [--msd] [Parser]
[--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>]
mdt [--gro] [--msd] [Parser]
[--t_steps <time steps>] [--min_window <min. time window>] [--dir <x, y, z>]
[--msd_mode atom --msd_species resname <resname> name <atom name>]
[--n_steps <start frame> <end frame>]
mdt [--gro] [--msd] [Parser]
[--t_steps <time steps>] [--min_window <min. time window>] [--dir <x, y, z>]
[--msd_mode atom --msd_species resname <resname> type <atom type>
resname <resname> type <atom type>] [--n_steps <start frame> <end frame>]
mdt [--gro] [--msd] [Parser]
[--t_steps <time steps>] [--min_window <min. time window>] [--dir <x, y, z>]
[--msd_mode atom --msd_species resname <resname> name <atom name>
resname <resname> name <atom name>] [--n_steps <start frame> <end frame>]mdt [--lam] [--msd] [Parser]
[--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>]
mdt [--lam] [--msd] [Parser]
[--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> <atom type>]
mdt [--lam] [--msd] [Parser]
[--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> <resname> type <atom type>]
mdt [--lam] [--msd] [Parser]
[--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> <resname>]Nernst-Einstein Conductivity
GROMACS
mdt [--gro] [--ne] [Parser]
[--t_steps <time steps>] [--skip_species <resname>] [--temp <temperature>]
[--n_steps <start frame> <end frame>] [--min_window <min. time window>]mdt [--lam] [--ne] [Parser]
[--t_steps <time steps>] [--dump_frame <steps>] [--n <frame stride>] [--temp <temperature>]
[--n_steps <start frame> <end frame>] [--min_window <min. time window>]Ion-Ion Correlations
GROMACS
mdt [--gro] [--corr] [Parser]
[--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>]mdt [--lam] [--corr] [Parser]
[--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 for slope>]Spatial Decomposition Analysis of Ion-Ion Correlations
GROMACS
mdt [--gro] [--spda] [Parser]
[--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>]mdt [--lam] [--spda] [Parser]
[--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 for slope>]Onsager Transport Coefficients
GROMACS
mdt [--gro] [--onsg] [Parser]
[--t_steps <time steps>] [--t_window <time window for slope>] [--temp <temperature>]
[--n_steps <start frame> <end frame>] [--n_delta <window for time origin shifting>]mdt [--lam] [--onsg] [Parser]
[--t_steps <time steps>] [--dump_frame <steps>] [--temp <temperature>]
[--n <frame stride>] [--t_steps <time steps>] [--t_window <time window for slope>]
[--n_steps <start frame> <end frame>] [--n_delta <window for time origin shifting>]Ionic Conductivity Using Stefan-Maxwell Diffusivity
GROMACS
mdt [--gro] [--smd] [Parser]
[--t_steps <time steps>] [--temp <temperature>]
[--n_steps <start frame> <end frame>] [--min_window <min. time window>]mdt [--lam] [--smd] [Parser]
[--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 Equation
GROMACS
mdt [--gro] [--en] [Parser]
[--t_steps <time steps>] [--t_window <time window for slope>]
[--n_steps <start frame> <end frame>] [--temp <temperature>]mdt [--lam] [--en] [Parser]
[--t_steps <time steps>] [--dump_frame <steps>] [--t_window <time window for slope>]
[--n <frame stride>] [--n_steps <start frame> <end frame>] [--temp <temperature>]Cluster Analysis
GROMACS
mdt [--gro] [--cage_p] [Parser]
[--t_steps <time steps>] [--n_steps <start frame> <end frame>] [--rcut <first solvation>]
[--resname <reference species> <target species>]mdt [--lam] [--cage_p <reference species> <cage species>] [Parser]
[--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
GROMACS
mdt [--gro] [--cage] [Parser]
[--ref_species <resname>] [--cage_species <resname>] [--n_steps <start frame> <end frame>]
[--t_steps <time steps>] [--rcut <first solvation>] [--steps <time origin steps>]mdt [--lam] [--cage] [Parser]
[--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
GROMACS
mdt [--gro] [--pcl] [Parser]
[--t_steps <time steps>] [--n_steps <start frame> <end frame>] [--steps <time origin steps>]
[--resname <reference species> <target species>]mdt [--lam] [--pcl] [Parser]
[--dump_frame <steps>] [--t_steps <time steps>] [--species <resname> <numbers>]
[--n <frame stride>] [--n_steps <start frame> <end frame>] [--steps <time origin steps>]
[--resname <reference species> <target species>]Transport Mechanism of Species
GROMACS
mdt [--gro] [--veh] [Parser]
[--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>]mdt [--lam] [--veh] [Parser]
[--t_steps <time steps>] [--dump_frame <steps>] [--min_window <min. time window>]
[--n <frame stride>] [--n_steps <start frame> <end frame>] [--temp <temperature>]
[--rcut <first solvation>] [--steps <time origin steps>]
[--resname <reference species> <target species>]Radial Distribution Function Calculation
COM-COM RDF
GROMACSmdt [--gro] [--rdf] [Parser]
[--t_steps <time steps>] [--n_steps <start frame> <end frame>] [--steps <time origin steps>]
mdt [--gro] [--rdf] [Parser]
[--rdf_mode com com --rdf_pairs resname <resname> type <atom type> <atom type> resname
<resname> type <atom type> <atom type>] [--t_steps <time steps>] [--n_steps <start frame>
<end frame>]
mdt [--gro] [--rdf] [Parser]
[--rdf_mode com com --rdf_pairs resname <resname> name <atom name> <atom name> resname
<resname> name <atom name> <atom name>] [--t_steps <time steps>] [--n_steps <start frame>
<end frame>]mdt [--lam] [--rdf] [Parser]
[--n <frame stride>] [--t_steps <time steps>] [--n_steps <start frame> <end frame>]
[--dump_frame <steps>] [--steps <time origin steps>]
mdt [--lam] [--rdf] [Parser]
[--dump_frame <steps>] [--t_steps <time steps>] [--n_steps <start frame> <end frame>]
[--n <frame stride>] [--rdf_mode com com --rdf_pairs resname <resname>
type <atom type> <atom type> resname <resname> type <atom type> <atom type>]ATOM-COM RDF
GROMACSmdt [--gro] [--rdf] [Parser]
[--rdf_mode atom com --rdf_pairs resname <resname> type <atom type> resname <resname> type
<atom type> <atom type>] [--t_steps <time steps>] [--n_steps <start frame> <end frame>]
mdt [--gro] [--rdf] [Parser]
[--rdf_mode atom com --rdf_pairs resname <resname> name <atom name> resname <resname> name
<atom name> <atom name>] [--t_steps <time steps>] [--n_steps <start frame> <end frame>]mdt [--lam] [--rdf] [Parser]
[--dump_frame <steps>] [--t_steps <time steps>] [--n_steps <start frame> <end frame>]
[--n <frame stride>] [--rdf_mode atom com --rdf_pairs resname <resname> type <atom type>
resname <resname> type <atom type> <atom type>]ATOM-ATOM RDF
GROMACSmdt [--gro] [--rdf] [Parser]
[--rdf_mode atom atom --rdf_pairs resname <resname> type <atom type> resname <resname> type
<atom type>] [--t_steps <time steps>] [--n_steps <start frame> <end frame>]
mdt [--gro] [--rdf] [Parser]
[--rdf_mode atom atom --rdf_pairs resname <resname> name <atom name> resname <resname> type
<atom name>] [--t_steps <time steps>] [--n_steps <start frame> <end frame>]mdt [--lam] [--rdf] [Parser]
[--dump_frame <steps>] [--t_steps <time steps>] [--n_steps <start frame> <end frame>]
[--n <frame stride>] [--rdf_mode atom atom --rdf_pairs resname <resname> type <atom type>
resname <resname> type <atom type>]ā³ Session Timer
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