Graphene Set Up

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 xyplane:

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:

Picture1

 

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:

Screen Shot 2018-02-27 at 19.58.06

 

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*