On Dec 10, 2014 10:21 PM, "Jackson Chief Elk" <jchief...@gmail.com> wrote: > > Hi, > I am building my own routine to use the Gromacs API to do MS-EVB. I need to treat O-H bonds of 1 hydronium ion with a Morse Potential. How can I specify in the *.mdp file, to just describe bonding in hydronium using this potential?
You can use morse=yes in the .mdp file, but this turns all bonds present in the molecular system into Morse ones. To use Morse selectively, the only solution is to put this information into the topology. Goog luck, Bogdan -- 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.
