gromacs-py 1.2.0

Gromacs_py is a python library allowing a simplified use of the gromacs MD simulation software.

Gromacs_py

Gromacs_py is a python library allowing a simplified use of the gromacs MD simulation software. Gromacs_py can build topologie based on a pdb file, create the simulation system (box, add water and ions) and run minimisation, equilibration and production run. One of the main objective of the gromacs_py wrapper is to automatize routine operations for MD simulation of multiple systems.

• Online Documentation:

  https://gromacs-py.readthedocs.io

• Source code repository:

  https://github.com/samuelmurail/gromacs_py

Main features:

• Python Scriptable simulation:

  • Topologie creation

  • Solvation

  • Ion insertion

  • Energy minimisation

  • Equilibration with position restraints

  • Production

  • GPU acceleration

• Topologie manipulation starting from a raw PDB:

  • Amino acid protonation and pKa calculation using apbs/pdb2pqr

  • Position constraints file .itp creation

  • Cyclic petide topologie

• Advanced simulation tools:

  • Monitor a simulation while running

  • Interrupt a simulation if a criterion is met (Not implemented yet)

Compatibility

• Supported Gromacs versions:

  • 2019*

  • 2018*

  • 2017

  • 2016

  • 5.1

  • 5.0

• Supported Python versions:

  • 3.8*

  • 3.7*

  • 3.6*

  • 3.5*

• Supported OS:

  • osx*

  • linux*

* tested after each code submission.

Quick install

If gromacs (version >= 5.1) is already install, then install you need to install the gromacs_py library, and add the gromacs gmx command in the environmnent variable $PATH:

pip install gromacs_py

# Add gromacs 'gmx' path:
export PATH='*path_to_gromacs*/bin/':$PATH

Tutorial

Here is an example of a short simulation of the SH3 domain of phospholipase Cγ1. Seven successive steps are used:

1. Topologie creation using create_top.py.

2. Minimisation of the structure using minimize_pdb.py.

3. Solvation of the system using solvate_ions.py.

4. Minimisation of the system using minimize_pdb.py.

5. Equilibration of the system using equi_3_step.py.

6. Production run using production.py.

7. Extension of the production run using extend.py.

# Create topologie
create_top.py -f gromacs_py/test/input/1y0m.pdb  -o tmp/1y0m/top -vsite

# Minimize the protein structure
minimize_pdb.py -f tmp/1y0m/top/1y0m_pdb2gmx_box.pdb -p tmp/1y0m/top/1y0m_pdb2gmx.top -o tmp/1y0m/em/  -n em_1y0m -nt 2

# Add water and ions
solvate_ions.py -f tmp/1y0m/em/em_1y0m_compact.pdb -p tmp/1y0m/top/1y0m_pdb2gmx.top -o tmp/1y0m_water_ions/top/  -n 1y0m_water_ions

# Minimize the system
minimize_pdb.py -f tmp/1y0m_water_ions/top/1y0m_water_ions_water_ion.gro -p tmp/1y0m_water_ions/top/1y0m_water_ions_water_ion.top -o tmp/1y0m_water_ions/em/  -n em_1y0m

# Do three small equilibrations with postion contraints on heavy atoms (first), Carbon alpha (second) and low constraint on Carbon alpha (third)
equi_3_step.py -f tmp/1y0m_water_ions/em/em_1y0m_compact.pdb -p tmp/1y0m_water_ions/top/1y0m_water_ions_water_ion.top -o tmp/1y0m_water_ions/  -n 1y0m -HA_time 0.1 -CA_time 0.1 -CA_LOW_time 0.1

# Small production run of 0.1 ns
production.py -f tmp/1y0m_water_ions/02_equi_CA_LOW/equi_CA_LOW_1y0m.gro -p tmp/1y0m_water_ions/top/1y0m_water_ions_water_ion.top -o tmp/1y0m_water_ions/03_prod -n 1y0m -time 0.1

# Extension of the simulation
extend.py -s tmp/1y0m_water_ions/03_prod/prod_1y0m.tpr -time 0.2

# Remove simulation files
rm -r ./tmp

Or simply use one command to do all previous commands:

top_em_equi_3_step_prod.py -f gromacs_py/test/input/1y0m.pdb -o tmp/1y0m -vsite -HA_time 0.1 -CA_time 0.1 -CA_LOW_time 0.1 -prod_time 0.3

Authors

• Samuel Murail, Associate Professor - Université Paris Diderot, CMPLI.

See also the list of contributors who participated in this project.

License

This project is licensed under the GNU General Public License v2.0 - see the LICENSE file for details.