[gmx-users] help on Graphene Nano Sheets

[Alex]

Justin, everything works for me with graphene/x2top under the latest
version. Am I doing something wrong? :)

On Wed, Apr 22, 2015 at 5:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/22/15 7:22 PM, marcello cammarata wrote:
>
>> yes, i used the Minoia tutorial,
>> i use a cnt_oplsaa at the first attempt, and forward i copied and modify
>> the
>> standard oplsaa folder. with both of them i have the same trouble.
>>
>>
> The seg fault will always occur with version 5.0.4; there is a bug we
> discovered a few weeks back:
>
> http://redmine.gromacs.org/issues/1711
>
> You'll need to use an older version (pre-5.0) for x2top to work properly
> (or patch the code and upload a fix to solve the bug :).
>
>    The inizial graphene layer was created using*VMD modelling toolbox*,
>> that was
>> a .pdb file, i convert it in .gro file using *editconf *command.
>> i open the gro file using Avogadro, and it is still a layer. But in the
>> gro file
>> the connections are loose.
>>
>
> CONECT entries in PDB files are rarely (never?) used in GROMACS.  They are
> totally irrelevant for the purpose of x2top.
>
> -Justin
>
>
>  here  i report the firt 5 rows of the graphene.gro file.
>>
>> UNNAMED
>>    112
>>      1GRA      C    1   0.000   0.000   0.000
>>      2GRA      C    2  -0.123   0.071   0.000
>>      3GRA      C    3  -0.123   0.213   0.000
>>      4GRA      C    4   0.000   0.284   0.000
>>      5GRA      C    5   0.246   0.000   0.000
>>
>> thanks
>>
>> Il 22/04/2015 19:46, Alex ha scritto:
>>
>>> Hello,
>>>
>>> The forcefields for CNT and graphene are identical (for the purpose of
>>> this discussion). Two questions:
>>>
>>> 1. Where did you get the initial graphene structure?
>>> 2. Are there any CONECT statements in it?
>>>
>>> I assume you used Andrea Minoia's guide and the contents of your
>>> cnt2_oplsaa.ff directory correspond to what he's got.
>>>
>>> Alex
>>>
>>> MC> Hi,
>>> MC> i am trying to model a Graphene nano sheet GNS on Gromacs-
>>> MC> I follow the advices about the nanotubes presented in the help site.
>>>
>>> MC> _http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube_
>>>
>>> MC> I run this command to greate the topology:
>>> MC> _g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa_
>>>
>>> MC> I got this error message:
>>>
>>> MC> GROMACS:      gmx x2top, VERSION 5.0.4
>>> MC> Executable:   /usr/local/gromacs/bin/gmx
>>> MC> Library dir:  /usr/local/gromacs/share/gromacs/top
>>> MC> Command line:
>>> MC>    g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa
>>>
>>> MC> Opening force field file
>>> MC>
>>> /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/atomnames2types.n2t
>>> MC> Opening force field file
>>> MC> /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/name_topology.n2t
>>> MC> There are 12 name to type translations in file cnt2_oplsaa.ff
>>> MC> Generating bonds from distances...
>>> MC> atom 112
>>> MC> There are 1 different atom types in your sample
>>> MC> Generating angles and dihedrals from bonds...
>>> MC> segmentazion fault (core dump created)
>>>
>>> MC> Someone can help me on this?
>>> MC> The graphene force field for nanolayer is the same for nanotube?
>>> There
>>> MC> is something that i have to change?
>>>
>>> MC> bests
>>>
>>> MC> --
>>> MC> Marcello Cammarata, Ph.D.
>>> MC> 3208790796
>>>
>>>
>>>
>>>
>>>
>>
> --
> ==================================================
>
> 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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