On 9/2/14, 10:13 PM, Kester Wong wrote:
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 0.5112.011
2 C 1 GRA C 2 0.5112.011
3 C 1 GRA C 3 0.5112.011
4 C 1 GRA C 4 0.5112.011
5 C 1 GRA C 5 0.5112.011
6 C 1 GRA C 6 0.5112.011
7 C 1 GRA C 7 0.5112.011
8 C 1 GRA C 8 0.5112.011
9 C 1 GRA C 9 0.5112.011
10 C 1 GRA C10 0.5112.011
11 C 1 GRA C11 0.5112.011
12 C 1 GRA C12 0.5112.011
13 C 1 GRA C13 0.5112.011
14 C 1 GRA C14 0.5112.011
15 C 1 GRA C15 0.5112.011
16 C 1 GRA C16 0.5112.011
17 C 1 GRA C17 0.5112.011
18 C 1 GRA C18 0.5112.011
19 C 1 GRA C19 0.5112.011
20 C 1 GRA C20 0.5112.011
21 C 1 GRA C21 0.5112.011
22 C 1 GRA C22 0.5112.011
23 C 1 GRA C23 0.5112.011
24 C 1 GRA C24 0.5112.011
25 C 1 GRA C25 0.5112.011
26 C 1 GRA C26 0.5112.011
27 C 1 GRA C27 0.5112.011
28 C 1 GRA C28 0.5112.011
29 C 1 GRA C29 0.5112.011
30 C 1 GRA C30 0.5112.011
31 C 1 GRA C31 0.5112.011
32 C 1 GRA C32 0.5112.011
33 C 1 GRA C33 0.5112.011
34 C 1 GRA C34 0.5112.011
35 C 1 GRA C35 0.5112.011
36 C 1 GRA C36 0.5112.011
37 C 1 GRA C37 0.5112.011
38 C 1 GRA C38 0.5112.011
39 C 1 GRA C39 0.5112.011
40 C 1 GRA C40 0.5112.011
41 C 1 GRA C41 0.5112.011
42 C 1 GRA C42 0.5112.011
43 C 1 GRA C43 0.5112.011
44 C 1 GRA C44 0.5112.011
45 C 1 GRA C45 0.5112.011
46 C 1 GRA C46 0.5112.011
47 C 1 GRA C47 0.5112.011
48 C 1 GRA C48 0.5112.011
49 C 1 GRA C49 0.5112.011
50 C 1 GRA C50 0.5112.011
51 C 1 GRA C51 0.5112.011
52 C 1 GRA C52 0.5112.011
53 C 1 GRA C53 0.5112.011
54 C 1 GRA C54 0.5112.011
55 C 1 GRA C55 0.5112.011
56 C 1 GRA C56 0.5112.011
57 C 1 GRA C57 0.5112.011
58 C 1 GRA C58 0.5112.011
59 C 1 GRA C59 0.5112.011
60 C 1 GRA C60 0.5112.011
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: 30.5944. Total charge
should normally be an integer.
Will the partial charge of graphene affect the NVT run, apart from slowing it
down?
The charges are unreasonable. The charges you find in ffnonbonded.itp have no
general meaning aside from the specific functional group from which they were
pulled. You're using the wrong atom types and charges, having taken both from
carbonyl carbon parameters. You should be using CA (aromatic carbon) with zero
charge on each.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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