Dear Lammps users.
I’m finding myself in need to solve a problem concerning a force-field for bisferrocene using a “dummy atom metod” described in
J. Phys. Chem. B 2006, 110, 33, 16640–16645.
I don’t know if a solution can be implemented within lammps.
The system is made by bisferrocene molecules added through the molecule command.
Each of the ciclopentadiene rings has a central dummy atom that binds to the central iron.
the dummy is a geometrical point computed at each step from the positions of the carbon atoms.
thus all the forces computed on the central atom at each step are transferred to the C1 and C2 atoms of the ring instead of directly acting as acceleration of the dummy atom and the position of the dummy atom is computed geometrically at each timestep from the position of the ciclopentadiene carbons.
I know nothing of cpp but I can handle python scripting
To sum up my problem is as follows:
I want to
- create x molecules of ferrocene with all the bonds/angles/dihedrals, including bonds linking the dummy atoms to the iron atoms and to the ring
- take the forces on the dummy atoms and add them to the fforces on the c1 and c2 atoms of the ring. then zero the forces on the dummy atom.
3)integrate to compute the positions and velocity for the following timestep
4)recompute the position of the dummy atom based on the position of the ring atoms.
iterate. Is there a way to do this with a combination of compute and fix or is it something that requires external scripting? in the second case where do I place my script in order to have the operations occur in the intended order?
Thank you in advance