[gmx-users] Graphene modeling

‪Mohammad Roostaie‬ ‪ mohammad.r0325 at yahoo.com
Tue May 16 13:32:07 CEST 2017

In addition, I used this command "gmx x2top -f g.gro -o g.top -ff cnt_oplsaa -name CNT -noparam" and I got this error:
Opening force field file ./cnt_oplsaa.ff/atomnames2types.n2tThere are 6 name to type translations in file ./cnt_oplsaa.ffGenerating bonds from distances...atom 46There are 1 different atom types in your sampleGenerating angles and dihedrals from bonds...Segmentation fault BestMohammad 

      From: ‪Mohammad Roostaie‬ ‪ <mohammad.r0325 at yahoo.com>
 To: Justin Lemkul <jalemkul at vt.edu>; gmx-users at gromacs.org 
 Sent: Tuesday, 16 May 2017, 13:59:29
 Subject: Re: [gmx-users] Graphene modeling
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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