You have: [ moleculetype ] A [atoms] 1 ... N
and [ moleculetype ] B [atoms] 1 ... M and want to make a bond between atom X of A and Y of B. So you have to merge A and B into: [ moleculetype ] A+B [atoms] 1 ... N N+1 ... N+M with a.o.: [bonds] X Y+N type bond-parameters. I hope this is clear enough. If it isn't, read Chapter 5 of the manual thoroughly. Cheers, Tsjerk On Wed, Apr 22, 2009 at 5:30 PM, He, Yang <yang...@mavs.uta.edu> wrote: > Hi Tsjerk, > > Thank you for your reply. SO you mean I can just define the bond in one > moleculetype.As what you said, I have to renumber all atoms from one of the > moleculetypes, > starting at N+1, with N being the number of the last atom of the first > moleculetype .Then I wonder which molecule type the atom N+1 belongs to . > Also, I wonder how to define the new atom N+1's moleculetype in the gro file > . I just am not sure about that. Can you give me much more information about > that? > > Thank you very much. > > Yang > ________________________________________ > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf > Of Tsjerk Wassenaar [tsje...@gmail.com] > Sent: Tuesday, April 21, 2009 11:22 PM > To: jalem...@vt.edu; Discussion list for GROMACS users > Subject: Re: [gmx-users] about the bond connection between different groups > > Hi He Yang, Justin, > >>> You have said bonds between distinct molecules require a merged topology. >>> Is >>> there any introduction in the manual or Do you have any example about the >>> merged topology? >>> >> >> A merged topology contains multiple moleculetype definitions in one >> topol.top. Discussions are in the archives. > > Bonds can only be defined within moleculetypes, not between them. So > you'll need to combine moleculetypes to create a bond between groups. > For this you have to renumber all atoms from one of the moleculetypes, > starting at N+1, with N being the number of the last atom of the first > moleculetype. You also have to renumber the indices for all other > blocks ([bonds], [angles], etc...). Then combine the blocks and > finally add the new bond. If it is a proper bond, you should also > consider adding the angles and dihedrals involved in the interaction. > Note again, merging to create a bond does not mean adding multiple > moleculetypes in one topol.top! > > Cheers, > > Tsjerk > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
