The simulation consists in a cubic box filled with water molecule. The force field for the water is tip4p/epsilon.
Execute generate_system.py using python to generate the initial configuration.
Then, run gromacs using
gmx grompp -f input/nvt.mdp -o nvt -pp nvt -po nvt
gmx mdrun -v -deffnm nvt
mv nvt.gro conf.gro
gmx grompp -f input/npt.mdp -o npt -pp npt -po npt
gmx mdrun -v -deffnm npt
mv npt.gro conf.gro
gmx grompp -f input/run.mdp -o run -pp run -po run
gmx mdrun -v -deffnm run
Execute the following command in the terminal:
gmx msd -f run.xtc -s run.tpr
Convert the trajectory to remove the periodic boundary conditions using:
gmx trjconv -f run.xtc -o trajectory.xtc -pbc nojump
Using python, run
python diff_coeff_mda.py
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