[gmx-users] Graphene modeling

[‪Mohammad Roostaie‬ ‪]

Hi Justin,
Thank you very much. It is Ok now.
Best,Mohammad

      From: Justin Lemkul <jalemkul at vt.edu>
 To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
 Sent: Tuesday, 16 May 2017, 18:34:14
 Subject: Re: [gmx-users] Graphene modeling
   


On 5/16/17 7:31 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> 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.n2t
> There are 6 name to type translations in file ./cnt_oplsaa.ff
> Generating bonds from distances...
> atom 46
> There are 1 different atom types in your sample
> Generating angles and dihedrals from bonds...
> Segmentation fault
>

Are you using the latest version of GROMACS?  There was an x2top seg fault fixed 
a few versions ago so using 2016.3 may be necessary here.

-Justin

> Best
> Mohammad
>
>
> --------------------------------------------------------------------------------
> *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
> <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.
> <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
>
> --
> ==================================================
>
> 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 <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
>
> ==================================================
>
>
>
>

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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