Hi, I am creating a topology for a molecule that is not defined by OPLS. I have some questions that I want to ask:
1. What is bondtype and ptype in ffnonbonded.itp? 2. If I use the Buckingham potential to define nonbonded interactions between atom A and atom B, does this potential apply to all A and B atoms in the system? For example, I have a molecule that has oxygen atoms. I define the Buckingham potential of oxygen atoms with various other atoms in an .itp file of this molecule. If I have water molecules as the solvent, how will the .itp file affect the interactions between water molecules? 2. When do I need [ pairs ] directive, and when do I not? If I use the buckingham potential, do I not need it? Best Regards, Dan -- 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.
