[gmx-users] help on Graphene Nano Sheets
Marcello Cammarata
marcello.cammarata at unipa.it
Thu Apr 23 10:24:36 CEST 2015
Thanks Justin, and thanks Alex.
If i have run the command x2top using pbd file but i got the same error.
which files have i substitute to my version ( Gro5.0) with the ones from
the pre-5 version?
Alex did you change something in your version? i am in ubuntu OS.
/GROMACS: gmx x2top, VERSION 5.0.4//
//Executable: /usr/local/gromacs/bin/gmx//
//Library dir: /usr/local/gromacs/share/gromacs/top//
//Command line://
// g_x2top -f Graphene15x15.pdb -o cnt.top -ff cnt2_oplsaa//
//
//WARNING: all CONECT records are ignored//
//Opening force field file
/usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/atomnames2types.n2t//
//Opening force field file
/usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/name_topology.n2t//
//There are 12 name to type translations in file cnt2_oplsaa.ff//
//Generating bonds from distances...//
//atom 112//
//There are 1 different atom types in your sample//
//Generating angles and dihedrals from bonds...//
//segmentation fauld (core dump created)/
if i want run the pdb file what command need i use? the same "x2top"?
could it work?
Il 23/04/2015 01:28, Alex ha scritto:
> 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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--
Marcello Cammarata, Ph.D.
3208790796
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