[gmx-users] Graphene modeling
mohammad.r0325 at yahoo.com
Tue May 16 11:29:37 CEST 2017
Thank you Justin,
Actually, I want to simulate a small box of water with graphene and protein. You mean that I should just build and put the .n2t file in the directory where I want to run the system, and no other files are required or should not be changed.
I used the files specified in this link: http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube
For example, for .n2t file:; Oplsaa-based n2t for carbon-based structures such as CNTs and graphenes
; Andrea Minoia
H HJ 0.00 1.008 1 C 0.109 ;Hydrogen
C CJ 0.00 12.011 3 C 0.142 H 0.109 H 0.109 ;Periferic C
C CJ 0.00 12.011 3 C 0.142 C 0.142 H 0.108 ;Periferic C
C CJ 0.00 12.011 1 C 0.142 ;Internal/periodic C
C CJ 0.00 12.011 2 C 0.142 C 0.142 ;Internal/periodic C
C CJ 0.00 12.011 3 C 0.142 C 0.142 C 0.142 ;Internal/periodic C
Thanks,Mohammad From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org; Mohammad Roostaie <mohammad.r0325 at yahoo.com>
Sent: Monday, 15 May 2017, 16:45:19
Subject: Re: [gmx-users] Graphene modeling
On 5/14/17 9:43 AM, Mohammad Roostaie wrote:
> Hi GROMACS users,
> I want to model a graphene sheet. I used the instruction stated in link http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube. I put the cnt_oplsaa.ff folder in the directory where I want to run the rest of the work. Also, I rename the residues of the graphene to “CJ” and the atoms to “C”. but, when I want to use “gmx x2top”, I get the error that says it cannot find any forcefield type for the atoms. Can you please help me to figure this out?
Since all you have are C atoms, this should require only a one-line .n2t file
(or addition to an existing one) that specifies the proper equilibrium bond
length for C-C in your structure. Without seeing your .n2t file and the x2top
screen output, there's nothing to suggest other than your .n2t file is somehow
inadequate for what you're trying to do.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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