[gmx-users] Creating an ITP file for charmm27
Justin Lemkul
jalemkul at vt.edu
Wed Sep 3 04:24:03 CEST 2014
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 0.51 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
>
> 34 C 1 GRA C 34 0.51 12.011
> 35 C 1 GRA C 35 0.51 12.011
> 36 C 1 GRA C 36 0.51 12.011
> 37 C 1 GRA C 37 0.51 12.011
> 38 C 1 GRA C 38 0.51 12.011
> 39 C 1 GRA C 39 0.51 12.011
> 40 C 1 GRA C 40 0.51 12.011
> 41 C 1 GRA C 41 0.51 12.011
> 42 C 1 GRA C 42 0.51 12.011
> 43 C 1 GRA C 43 0.51 12.011
> 44 C 1 GRA C 44 0.51 12.011
> 45 C 1 GRA C 45 0.51 12.011
> 46 C 1 GRA C 46 0.51 12.011
> 47 C 1 GRA C 47 0.51 12.011
> 48 C 1 GRA C 48 0.51 12.011
> 49 C 1 GRA C 49 0.51 12.011
> 50 C 1 GRA C 50 0.51 12.011
> 51 C 1 GRA C 51 0.51 12.011
> 52 C 1 GRA C 52 0.51 12.011
> 53 C 1 GRA C 53 0.51 12.011
> 54 C 1 GRA C 54 0.51 12.011
> 55 C 1 GRA C 55 0.51 12.011
> 56 C 1 GRA C 56 0.51 12.011
> 57 C 1 GRA C 57 0.51 12.011
> 58 C 1 GRA C 58 0.51 12.011
> 59 C 1 GRA C 59 0.51 12.011
> 60 C 1 GRA C 60 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?
>
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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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