Dear gmx-users,
I have manually created a graphene.itp file for charmm27 forcefield calculations, with the intention to model the contact angle of water.
The atomic mass and charge values were obtained from the forcefield ffnonbonded.itp.
Could anyone please advise if my file is correct?
[ moleculetype ]
;name nrexcl
GRA 3
[ atoms ]
; id at type resnum resname atname cg no charge mass
1 C 1 GRA C 1 0.51 12.011
2 C 1 GRA C 2 0.51 12.011
3 C 1 GRA C 3 0.51 12.011
4 C 1 GRA C 4 0.51 12.011
5 C 1 GRA C 5 0.51 12.011
6 C 1 GRA C 6 0.51 12.011
7 C 1 GRA C 7 0.51 12.011
8 C 1 GRA C 8 0.51 12.011
9 C 1 GRA C 9 0.51 12.011
10 C 1 GRA C 10 0.51 12.011
11 C 1 GRA C 11 0.51 12.011
12 C 1 GRA C 12 0.51 12.011
13 C 1 GRA C 13 0.51 12.011
14 C 1 GRA C 14 0.51 12.011
15 C 1 GRA C 15 0.51 12.011
16 C 1 GRA C 16 0.51 12.011
17 C 1 GRA C 17 0.51 12.011
18 C 1 GRA C 18 0.51 12.011
19 C 1 GRA C 19 0.51 12.011
20 C 1 GRA C 20 0.51 12.011
21 C 1 GRA C 21 0.51 12.011
22 C 1 GRA C 22 0.51 12.011
23 C 1 GRA C 23 0.51 12.011
24 C 1 GRA C 24 0.51 12.011
25 C 1 GRA C 25 0.51 12.011
26 C 1 GRA C 26 0.51 12.011
27 C 1 GRA C 27 0.51 12.011
28 C 1 GRA C 28 0.51 12.011
29 C 1 GRA C 29 0.51 12.011
30 C 1 GRA C 30 0.51 12.011
31 C 1 GRA C 31 0.51 12.011
32 C 1 GRA C 32 0.51 12.011
33 C 1 GRA C 33 0.51 12.011
In the tutorial by Andrea Minoia (http://chembytes.wikidot.com/grocnt), all the charges of graphene were set to zero, but I have decided to keep the graphene surface charges.
Has anyone looked at the difference between the water/graphene interaction, having a charged graphene .itp file as opposed to zero charge itp?
When creating the tpr file for energy minimisation: gmx_mpi grompp -f em.mdp -c graphene_.gro -n system.ndx -o topol.tpr
I received this: System has non-zero total charge: 30.59999944. Total charge should normally be an integer.
Will the partial charge of graphene affect the NVT run, apart from slowing it down?
Regards,
Kester
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