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# <sukriti...@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@N) > | Nanyang Technological University > Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, > Singapore(637459) > Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web: > erian.ntu.edu.sg > > ________________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of abhijit > Kayal <abhijitchemi...@gmail.com> > Sent: Thursday, July 3, 2014 6:43 PM > To: gmx-us...@gromacs.org; vvcha...@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 <vvcha...@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 <jalem...@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 > > > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > http://mackerell.umaryland.edu/~jalemkul > > > > > > ================================================== > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a > > > mail to gmx-users-requ...@gromacs.org. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > Abhijit kayal > Research Scholar > Theoretical Chemistry > IIT Kanpur > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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