[gmx-users] help on Graphene Nano Sheets

Marcello Cammarata marcello.cammarata at unipa.it
Thu Apr 23 17:08:26 CEST 2015


I run a graphene nanolayer, usin the below description (from previous mail.
Now i got an other error.  It look like there is a conflict in a force 
field system, someone can suggest me how to modify it?
the force field file came from Minoia advices, reported in the web side!
/
//Program grompp, VERSION 4.6.7//
//Source code file: 
/home/marcello/DATI/software/gromacs-4.6.7/src/kernel/topio.c, line: 752//
//
//Fatal error://
//Syntax error - File forcefield.itp, line 31//
//Last line read://
//'1               3               yes             0.5     0.5'//
//Found a second defaults directive./*
*

Thanks

Il 23/04/2015 14:35, Marcello Cammarata ha scritto:
> 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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