Steered molecular dynamics - problem med att få till "the pulling groups".

(Jag hade ingen aning om vart jag skulle placera denna - ber om ursäkt om den hamnar helt fel!)

På engelska men jag hoppas att det är okej ändå:

I'm trying to perform a steered molecular dynamics simulation where I pull a magnesium ion from two amino acids. The amino acids are on either side of a protein dimer interphase and the magnesium ion is between them. The amino acids both have a COO- group at the end.

I the first run I had the four oxygen atoms as one group and the magnesium ion as the other group. The result was that the magnesium ion was stuck to one of the oxygens through the entire simulation.

In the second run I split the oxygens into four groups and the magnesium ion was the fifth. Now the magnesium is still attached to an oxygen, but the magnesium does leave this site and moves further from it during the simulation.

What I do need it the magnesium ion to be attacted to all the four oxygens and to be pulled away from it.

The starting frame is a pdb-frame where the magnesium ion is positioned almost exactly in the center between all of the oxygens. But the starting frame of the simulation is with the magnesium ion positioned stuck to an oxygen atom.

Any advice on what to adjust?

Regarding spring constant and pulling velocity. I can of course adjust, run and see what happens. But I rather not as I am running on a budget of a computational group where I'm doing an internship. Here it to me doesn't feel like it is the spring constant or pulling velocity that is the issue, as the issue is that the magnesium doesn't seem to be attracted to all oxygens. But could the spring constant and velocity be the issue?

Could the following be the issue and the solution to remove the periodic boundary conditions? From a information page about SMD and non-equilibrium pulling: "In GROMACS, there are three ways to define the center of mass of a group. The standard way is a “plain” center of mass, possibly with additional weighting factors. With periodic boundary conditions it is no longer possible to uniquely define the center of mass of a group of atoms. Therefore, a reference atom is used. For determining the center of mass, for all other atoms in the group, the closest periodic image to the reference atom is used. This uniquely defines the center of mass. By default, the middle (determined by the order in the topology) atom is used as a reference atom, but the user can also select any other atom if it would be closer to center of the group."

I have very little experience in SMD and do not yet understand everything about what I bring up above. I've had bad luck with my supervisor being ill a lot in the past month and later very busy trying to catch up so I haven't had the possibility to ask things e.g. about spring constants or velocity which I don't yet understand. I'm not after someone giving me the answers but hints to what to look at are very much appreciated.