[gmx-users] Parameterizing Dummy Atoms (4fd)

[Benjamin Joseph Coscia]

Hi Gromacs users,

I have been working to implement dummy atoms in a system that needs to be
cross-linked. The cross-linking reaction generates atoms in my system due
to the reaction with initiator. I am trying to implement dummy atoms in my
system so that they can become real hydrogen atoms when cross-linking
occurs.

Based on my system, I have determined that 4fd would probably be the best
construction, even though it is the slowest. I understand how to set up the
dummy atoms in my topology. I believe that parameter 'd' from section 5.2.2
of the Gromacs manual is the same as 'c' from equation (4.125) in the
manual (correct me if I'm wrong). My question is whether there is a simple
way to determine the a and b parameters that go along with function type 1.
I've done some calculations and it is clear that this equation maintains
the distance which is defined by 'd' in the topology file.

My problem is coming up with 'a' and 'b'. I tried 0.33333 for both as shown
in the manual just to see what would happen. Energy minimization converges
but pushes one of the dummy atoms very far from the molecule it belongs to.
If I try any simulation after that, it diverges. I've tried a few
combinations with the same results. I'm working to back calculate a and b
based on where I think the dummy atom should stay situated.

Is there a better approach?

Thanks!
Ben Coscia