MD simulation of bulk BMPyrDCA ionic liquid

Simple demonstration of a molecular dynamics simulation of 25 BMPyrDCA ionic pairs in a box.

Inputs (packmol.inp, STEEP.mdp, RUN.mdp, topol.top) and force field parameters: github.com/vilab-tartu/LOKT.02.048/tree/master/MD_BMPyrDCA_box. The force fields are taken from github: github.com/vladislavivanistsev/RTIL-FF. References are given within the files.

Let’s execute some commands to tell the computer how to run the simulation. First, we pack 25 BMImDCA into a predefined box. For packmol we should thank J. M. Martínez and L. Martínez. Visit m3g.iqm.unicamp.br/packmol/ to see details. In case packmol does not work, I have put packmol.gro file.
./packmol < packmol.inp
gmx editconf -f packmol.pdb -o packmol.gro

Now let’s create an index of the ionic pairs. Enter q.
gmx make_ndx -f packmol.gro -o index.ndx

Prepare an executable file for the simulation.
gmx grompp -f STEEP.mdp -c packmol.gro -p topol.top -n index.ndx -o STEEP

Execute the first simulation step.
gmx mdrun -deffnm STEEP

Prepare another executable file for the simulation.
gmx grompp -f RUN.mdp -c STEEP.gro -p topol.top -n index.ndx -o NVT

Run the simulation, so-called production run. Note, it should use all available CPUs.
gmx mdrun -deffnm NVT

Convert the trajectory for the whole system. Enter 0.
gmx trjconv -f NVT.xtc -s NVT.tpr -o NVT.trr -ur compact -pbc mol

To see the equilibrated system, open a terminal and type “vmd NVT.gro”. In the “VMD main” window select the single line “0 T A D F NVT.gro …”, then from File menu choose “load data into molecule”, select “NVT.trr” file.
vmd NVT.gro

Examine the spatial distribution. For example select group 2 and then 3 to see the destribution of 3 (DCA anion) around 2 (Pyr cation).
gmx spatial -f NVT.xtc -s NVT.tpr -n index.ndx

Visualize the grid.cude in VMD. Chech the representations and drawing method: isosurface.
vmd grid.cube

You can do much more when you have a longer trajectory. For example, you may calculate density or diffusion coefficient.