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-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
