[gmx-users] Graphene topology file

#SUKRITI GUPTA# SUKRITI002 at e.ntu.edu.sg
Mon Jul 7 06:36:31 CEST 2014 

Hi all,

After getting the topology file for graphene, when i tried to freeze graphene and do energy minimization with just water molecules around it, then the graphene structure becomes distorted ie. the upper layer of the graphene shifts down and the terminal carbons forms bond with each other. I think this happens because i did not add terminal hydrogens to the graphene sheet as I wanted periodic boundary conditions in x y direction. Also the box size in z direction is shown to be zero in the output file of energy minimization. Can anyone please let me know how to solve this problem?

Thanks,
 
Sukriti

________________________________

Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N) | Nanyang Technological University
Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459)
Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:erian.ntu.edu.sg

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg>
Sent: Friday, July 4, 2014 5:10 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Graphene topology file

Hi Abhijit,

Thanks for the reply. Now it is working.

Regards
Sukriti



________________________________

Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N) | Nanyang Technological University
Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459)
Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:erian.ntu.edu.sg

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of abhijit Kayal <abhijitchemiitd at gmail.com>
Sent: Friday, July 4, 2014 4:14 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Graphene topology file

 Hi Sukirti,

Try the following and additionally if you want force and angle constant you
can also mention in g_x2top.
g_x2top -f gra.pdb -o gra.top -name  GRA -nexcl 3 -pbc

 You have to mention periodic_molecules=yes in the .mdp file.

Thanks
Abhijit


On Fri, Jul 4, 2014 at 1:04 PM, #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg>
wrote:

> Hi Abhijit,
>
> My g_x2top command is:
> g_x2top -f gra_2.pdb -o graphene.top -ff oplsaa -name graphene -noparam
> -pbc
>
> The grompp output is:
>
> ERROR 4100 [file graphene.top, line 10448]:      ; (for all the lines, I
> have copied here only one line.)
>   No default Ryckaert-Bell. types
>
> Excluding 3 bonded neighbours molecule type 'graphene'
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/kernel/toppush.c, line:
> 1987
>
> Fatal error:
> No such moleculetype SOL
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Thanks
> Sukriti
>
> ________________________________
>
> Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N)
> | Nanyang Technological University
> Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive,
> Singapore(637459)
> Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:
> erian.ntu.edu.sg
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of abhijit
> Kayal <abhijitchemiitd at gmail.com>
> Sent: Friday, July 4, 2014 2:21 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Graphene topology file
>
> Hi Sukriti,
>    Can you tell me the g_x2top command you have given and the grompp
> output.
>
> Thanks
> Abhijit
>
>
> On Fri, Jul 4, 2014 at 10:01 AM, #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg>
> wrote:
>
> > Dear Justin and Abhijit,
> >
> > Thanks a lot for your help. Now I am able to make the topology file but
> > while doing grompp for energy minimisation its not taking the dihedral
> > values on its own.
> >
> > Regards
> > Sukriti
> > ________________________________
> >
> > Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N
> )
> > | Nanyang Technological University
> > Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive,
> > Singapore(637459)
> > Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:
> > erian.ntu.edu.sg
> >
> > ________________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of abhijit
> > Kayal <abhijitchemiitd at gmail.com>
> > Sent: Thursday, July 3, 2014 6:43 PM
> > To: gmx-users at gromacs.org; vvchaban at gmail.com
> > Subject: Re: [gmx-users] Graphene topology file
> >
> > Hi Sukriti,
> >  Copy the oplsaa.ff directory to your working directory. Then in
> > ffnonbonded.itp file add the following lines..
> >  opls_995   C      6    12.01100     0.000       A    3.40000e-01
> > 3.61200e-01
> >  opls_996   C      6    12.01100     0.000       A    3.40000e-01
> > 3.61200e-01
> >  opls_997   C      6    12.01100     0.000       A    3.40000e-01
> > 3.61200e-01
> >
> > Then in   atomname2type.n2t file add the following lines.
> > C    opls_995    0      12.011  2    C  0.142  C 0.142
> > C    opls_996    0      12.011  3    C  0.142  C 0.142  C 0.142
> > C    opls_997    0      12.011  1    C  0.142
> >
> > Then use g_x2top. This will work.
> >
> > Thanks
> >  Abhijit
> >
> >
> > On Thu, Jul 3, 2014 at 3:11 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>
> > wrote:
> >
> > > Graphene topology is like for tube, so
> > >
> > > C .... C
> > > C ... C ... C
> > > C .... C  ....C  .... C
> > >
> > > to the N2T file and you are done.
> > >
> > >
> > > Dr. Vitaly V. Chaban
> > >
> > >
> > > On Wed, Jul 2, 2014 at 5:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> > > >
> > > >
> > > > On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote:
> > > >>
> > > >> Dear all,
> > > >>
> > > >>
> > > >> I want to simulate graphite in water, for which i am trying to
> create
> > a
> > > >> topology file for graphite. As its .rtp file cannot be written
> > > correctly, i
> > > >> tried to use g_x2top command following the steps given in following
> > > >> tutorial.
> > > >>
> > > >> http://chembytes.wikidot.com/grocnt
> > > >>
> > > >>
> > > >> But I think this tutorial is quite old and hence suitable for older
> > > >> version of gromacs as it still uses FF.dat file. Moreover if i am
> > > trying to
> > > >> make a new forcefield directory with name graphite_oplsaa containing
> > the
> > > >> modified files like .n2t,.rtp and .itp, its giving me an error that
> > > "Could
> > > >> not find force field 'graphite_oplsaa' in current directory, install
> > > tree or
> > > >> GMXDATA path". When I try to add this forcefield in original path
> ie.
> > > >> user/share/gromacs/top, it does not allow me to do that as i am not
> > the
> > > >> administrator. Can anyone please let me know how to create the
> > topology
> > > >> file. I require 3 graphene sheets with pbc. I have created the .pdb
> > file
> > > >> using nanobuilder in vmd.
> > > >>
> > > >
> > > > The tutorial is indeed outdated but the logic is fairly sound.  You
> > don't
> > > > have to modify anything in $GMXLIB (system-wide); you can just create
> > an
> > > > .n2t file in the working directory and it will override the one at
> the
> > > force
> > > > field level.
> > > >
> > > > -Justin
> > > >
> > > > --
> > > > ==================================================
> > > >
> > > > Justin A. Lemkul, Ph.D.
> > > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > > >
> > > > Department of Pharmaceutical Sciences
> > > > School of Pharmacy
> > > > Health Sciences Facility II, Room 601
> > > > 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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> >
> > --
> > Abhijit kayal
> > Research Scholar
> > Theoretical Chemistry
> > IIT Kanpur
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>
>
> --
> Abhijit kayal
> Research Scholar
> Theoretical Chemistry
> IIT Kanpur
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--
Abhijit kayal
Research Scholar
Theoretical Chemistry
IIT Kanpur
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