Hi Sukriti, Can you post your .mdp file of energy minimization? The problem is not because there are no terminal H atoms. If you want periodic boundary conditions only x-y direction then you have to use nwall in .mdp file.
Thanks Abhijit On Mon, Jul 7, 2014 at 10:06 AM, #SUKRITI GUPTA# <sukriti...@e.ntu.edu.sg> wrote: > 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@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 #SUKRITI > GUPTA# <sukriti...@e.ntu.edu.sg> > Sent: Friday, July 4, 2014 5:10 PM > To: gmx-us...@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@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: Friday, July 4, 2014 4:14 PM > To: gmx-us...@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# <sukriti...@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@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: Friday, July 4, 2014 2:21 PM > > To: gmx-us...@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# < > 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? 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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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