Build the system:

The system contains 2 C240 “buckyball” solvated in water. From literature we know the diameter of C240 is 1.5 nm. Hence, to understand the interaction between two C240 molecules we take a box size of 4x4x6. To prevent water from being added inside the C240 spheres, 2 “dummy” atoms are placed (gmx insert-molecule -ip position.dat) at the center of the C240 spheres, and then solvated with an exclusion radius of 0.75nm (gmx solvate -radius 0.75). Dummy atom is removed using gmx trjconv. C240 is then placed in the box using gmx insert-molecule. The van der Waals radii was set to 0 (-scale 0) during insertion as the molecule is very large and interacts with surrounding water molecule.

Similar method has been used to insert 1mol/L of NH₄NO₃.

Equilibration of the system:

Equilibration is done with a standard protocol of energy minimization, followed by NVT and NPT simulation for 100 ps each.  The position of the C240 should be frozen for energy minimization and NVT simulation with:

freezegrps = C24
freezedim = Y Y Y

Pulling in NPT simulation:

For NPT simulation, if position of C240 is fixed then the water molecules will move apart as the volume of the system is not fixed and water molecule between the particles are less energetically favorable. To fix the position of C240s, a soft potential is used for both C240 with pull option:

pull=yes
pull-ngroups=2
pull-group1-name=C24_1
pull-group2-name=C24_2
pull-ncoords=2

pull-coord1-type=umbrella
pull-coord1-geometry=distance
pull-coord1-groups=0 1
pull-coord1-origin=2 2 1.5
pull-coord1-dim=Y Y Y
pull-coord1-k=6000

pull-coord2-type=umbrella
pull-coord2-geometry=distance
pull-coord2-groups=0 2
pull-coord2-origin=2 2 4.5
pull-coord2-dim=Y Y Y
pull-coord2-k=6000

Using type umbrella and spring constant 6000 we allow the COM of the particle to move around a fixed position by only 0.1 Å . The index file is edited to identify the two C240 molecules as C24_1 and C24_2.