Dear all,

I have tried to simulate graphene sheet as written in the website (https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up).

The reason I am trying to simulate the sheet, I want to add the graphene sheet as a substrate in a cubic box and evaporate some molecules on it. Unfortunately, I had a problem while trying to  run energy minimization using  (gmx grompp -f minim.mdp -c GRM_w.gro -p grm_w.top -o min1.tpr) I got the below error: Fatal error: number of coordinates in coordinate file (GRM_w.gro, 146535)              does not match topology (grm_w.top, 156815).

some differences between my simulation and the one in the website:

1. I am using gromos54a7 instead of charmm36. The reason for using gromos 54a7 that I will need to evaporate some molecules on the graphene sheet and they should be evaporated using gromos 54a7.

2. I am using GRM instead of GRA.The reason for using the GRM is that I found the graphene sheet.itp online for the gromos 54a7 and it was named GRM and hence, I had to name everything GRM to match the names in the .itp that I included.

The steps I did using the terminal on Linux :

1. cd and go to directory

2. create a text file named GRM.gro and paste the data belwo in the file:

GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring

4

1GRM C1 1 0.061 0.071 0.000

1GRM C2 2 0.184 0.142 0.000

1GRM C3 3 0.184 0.284 0.000

1GRM C4 4 0.061 0.355 0.000

0.245951 0.426000 0.284000

3. gmx genconf -f GRM.gro -o GRM_sheet.gro -nbox 15 10 1

create the graphene sheet

4. I created the file graphene.n2t and attached the below

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

5. I created a new file named grm_w.top and included the forcefield, the water model spc and the graphene sheet.itp that I found it online.

; Include forcefield parameters

#include "/home/abdelaal/Desktop/GROMACS/C60-TAPC/GRAPHENE/gromos54a7.ff/forcefield.itp"

; Include topology for GRA

#include "/home/abdelaal/Desktop/GROMACS/C60-TAPC/GRAPHENE/GRM4x.itp"

; Include water topology

#include "/home/abdelaal/Desktop/GROMACS/C60-TAPC/GRAPHENE/gromos54a7.ff/spc.itp"

[ system ]

; Name

GRM in water

[ molecules ]

; Compound #mols

GRM 1

SOL 50

6. I chanegd the size of the sheet in the z direction using:

gmx editconf -f GRM_sheet.gro -o GRM_sheet_new.gro -box 10 15 10

7. I solvate the system using:

gmx solvate -cp GRM_sheet_new.gro -o GRM_w.gro -p grm_w.top

now the topology file grm_w.top was updated and a line was added as below:

; Include forcefield parameters

#include "/home/abdelaal/Desktop/GROMACS/C60-TAPC/GRAPHENE/gromos54a7.ff/forcefield.itp"

; Include topology for GRA

#include "/home/abdelaal/Desktop/GROMACS/C60-TAPC/GRAPHENE/GRM4x.itp"

; Include water topology

#include "/home/abdelaal/Desktop/GROMACS/C60-TAPC/GRAPHENE/gromos54a7.ff/spc.itp"

[ system ]

; Name

GRM in water

[ molecules ]

; Compound #mols

GRM 1

SOL 50

SOL 48595

now I have 2 SOL which I don’t know what should I do.

8. I included in my minim.mdp file a line with : Periodic_molecules = yes

9. I tried to run energy minimization using:

gmx grompp -f minim.mdp -c GRM_w.gro -p grm_w.top -o min1.tpr

and I got an error:

Fatal error:

number of coordinates in coordinate file (GRM_w.gro, 146535)

does not match topology (grm_w.top, 156815)

END of steps.

I read that if the difference between the 2 numbers is devisable by 3, it means that the problem in the solvate and you can change the number manually to match the other one. But it is not the case here. I also thought that the problem might be that I have 2 SOL lines in the .top and I removed the SOL 50 line but the difference decreased by 149 only.

Looking forward for your help, I have been trying for many days without success.

Attached are all the files I used it including steps file which contains all the steps I did as written above.