[gmx-users] Graphene topology file
#SUKRITI GUPTA#
SUKRITI002 at e.ntu.edu.sg
Fri Jul 4 11:10:34 CEST 2014
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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