Hi Blake,
I think the “appropriate” LJ parameters for the carboxylate group
depend on the counter-ion and on the specific details that you want to
study. There is a paper by Project (J Comput Chem 29: 1163–1169, 2008)
that focuses on the interactions of peptide side-chains with calcium
ions which presents some optimised OPLS-AA LJ parameters for the
interactions between calcium ion and the oxygen atoms of the
carboxylate group. I myself have tried to further optimise these
parameters as well (manuscript under review).
Cheers,
Jens
--
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 [email protected].
