Generate PEG topology for GROMACS and LAMMPS

Description

Python scripts for generating a single all-atom PEG molecule with a number Nseg of monomer. The charmm36 force field is used, and the output is readable by GROMACS and LAMMPS.

How to (for GROMACS):

Generate the configuration files using generatePEGgromacs.ipynb, or simply by executing generatepeg.sh from the GROMACS folder:

    sh generatepeg_gromacs.sh

You can vary the number of monomer by changing the value of Nseg. Then, minimize the energy of the PEG using GROMACS:

    gmx grompp -f input/em.mdp -o em -pp em -po em
    gmx mdrun -v -deffnm em
    mv em.gro conf.gro

Eventually, you can relaxe the PEG molecule in the NVT ensemble:

    gmx grompp -f input/nvt.mdp -o nvt -pp nvt -po nvt
    gmx mdrun -v -deffnm nvt

Output (GROMACS)

Pre-equilibrated topology files are given here :

• PEG200
• PEG600
• PEG1200

This video has been made using the PEG molecule generated with this script.

Contact

Feel free to contact me by email if you have inquiries. You can find contact details on my personal page.