[gmx-users] help on Graphene Nano Sheets

Thu Apr 23 13:50:50 CEST 2015

On 4/23/15 4:24 AM, Marcello Cammarata wrote:
> 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?

The command is the same; if you're getting a seg fault in 5.0.4 you need to use 
version 4.6.7.

-Justin

> 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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>

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

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

==================================================