[gmx-users] help on Graphene Nano Sheets

Marcello Cammarata marcello.cammarata at unipa.it
Thu Apr 23 14:35:46 CEST 2015 

i unistalled GRO 5 and installed GRO4.6.7_
i run the  x2top and i got this message:/

//Opening force field file 
/usr/local/gromacs/share/gromacs/top/cnt_oplsaa.ff/atomname2type.n2t//
//There are 32 name to type translations in file cnt_oplsaa.ff//
//Generating bonds from distances...//
//atom 112//
//There are 1 different atom types in your sample//
//Generating angles and dihedrals from bonds...//
//Before cleaning: 672 pairs//
//Before cleaning: 672 dihedrals//
//There are  168 proper dihedrals,    0 impropers,  336 angles//
//           504 pairs,      168 bonds and   112 atoms//
//Total charge is 0, total mass is 1345.23//
//
//WARNING: topologies generated by g_x2top can not be trusted at face 
value.//
//         Please verify atomtypes and charges by comparison to other//
//         topologies/*.*

I am enough happy because it now work.  (i have just to reset the 
polymer residue that i had defined in GRO5).
But i got a warning, how i can correct this warning. I don't know the 
type of error!




Il 23/04/2015 13:50, Justin Lemkul ha scritto:
>
>
> 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
>>>>
>>>> ==================================================
>>>> -- 
>>>> Gromacs Users mailing list
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>>
>

-- 
Marcello Cammarata, Ph.D.
3208790796

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