I am simulating a polymer using the OPLS forcefield. The polymer has a sidechain with a secondary amide. Using the atom charges given in the forcefield, the amide group (N, O, 2Cs, 2 Hs) has a net negative charge. I don't understand why this is so, since to my knowledge amides are not generally negatively charged. When repeated several times, the sidechain gives my polymer a net negative charge, when in real life the polymer is neutral.
I'm not sure what to do. I don't want to just arbitrarily adjust the charges in the forcefield, but I don't understand why the forcefield charges work out this way unless the forcefield is flawed. Can I just slightly adjust the charges in the amide group to come out neutral. That seems... wrong. -- 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.
