[gmx-users] Re: OPLS-AA: LJ problem? Atoms overlapping...

[Christopher Rowan]

Here are some more details:

My cg minimized structure has a distance of 0.3 Angstroms between Ag
and another atom of another molecule.
Changing all my Ag to hydrogens and running a cg still gives a
distance of 0.3 Angstroms.

I could also add that each Ag belongs to its own charge group, so they
should be "felt".
I've tried starting with a different geometry as well with similar results.

Files were modified as follows:

ffoplsaa.atp  I added Silver as:

 AG        107.87

ffoplsaanb.itp  I've added:

 AG         AG     47   107.8700     0.000       A    2.80455e-01  1.73304e-01

Chris Rowan