[gmx-users] Morse potential for Specific Group

[Bogdan Costescu]

On Dec 10, 2014 10:21 PM, "Jackson Chief Elk" <jchiefelk at 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