Python scripts for generating a single all-atom PEG (-OH terminated) or PEG (-CH3 terminated) molecule with a number Nseg of monomer. The charmm36 force field is used, and the output is readable by GROMACS and LAMMPS.
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
Pre-equilibrated topology files are given here :
This video has been made using the PEG molecule generated with this script.
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