Example Protocol: Graphene Sheet in Water
This example has been kindly provided by Shansi Thian.
1. Create a new working directory GRAPHENE. Copy charmm36.ff forcefield file into it.
2. Write a unit cell file, named GRA.gro, and copy the following content into it:
GRA: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring 4 1GRA C1 1 0.061 0.071 0.000 1GRA C2 2 0.184 0.142 0.000 1GRA C3 3 0.184 0.284 0.000 1GRA C4 4 0.061 0.355 0.000 0.245951 0.426000 0.284000
3. Create a sheet of graphene in xy–plane:
gmx genconf -f GRA.gro -o GRA_sheet.gro -nbox 15 10 1
4. Build the topology file:
A. Create a new file in charm36.ff, called graphene.n2t. This file contains specific parameters for your system. Copy information into it:
C CG2R61 0.00 12.011 1 C 0.142 C CG2R61 0.00 12.011 2 C 0.142 C 0.142 C CG2R61 0.00 12.011 3 C 0.142 C 0.142 C 0.142
B. Generate a topology for your system
gmx x2top -f GRA_sheet.gro -o gra.top -name GRA -nexcl 3 -ff charmm36 -kb 255224 -kt 334.72 -kp 12.9704 –alldih
C. Create from gra.top GRA.itp, by removing a header until [ moleculetype ] and the description of [ system ] and [ molecules ], as sown by selection below:
D. create a new .top file, including links to all the forcefield and .itp files needed for your work. In this example, tip4p water has also been included as following:
E. Change the size of the box in z-direction, this will create a vacuum, that you can then fill up with water.
F. Solvate the system, number of waters will automaticaly be updated in .top file
gmx solvate -cp GRA_sheet -o GRA_w.gro -p gra-w.top
Now you have a system ready for simulation!
You can now run energy minimization:
make sure to include periodic_molecules = yes in your .mdp file
gmx grompp -f min.mdp -c GRA_w.gro -p gra-w.top -o min1.tpr gmx mdrun -v -deffnm min1
*Please note that CHARMM36 force field has not been tested by authors for modeling of graphene, and is used here solely for the purpose of the tutorial*
Alternatively, see this code on GitHub (with amendments by Valentina) – tutorial soon!