I want to simulate simple system of 3 charges in equilateral triangle with the side L. Also the distances between “central” and two other charges need to be fixed and equal to L.
When I run simulations without bonds everything is fine and charges repel as they should.
However when I add bonds and/or use fix shake charges cease to move. Also if I add fourth charge near the triangle simulation again looks normal.
Could you please help ?
data_file.txt (279 Bytes)
inp.txt (538 Bytes)
you are not initializing any velocities, so atoms will not move, if the net forces cancel or are removed. when using fix shake bond distances are fixed, so there cannot be any net force on any of the atoms due to the geometry and bond constraints.
when using bonded interactions, the special_bonds factors apply. i.e. with the default setting of the scaling factors, all 1-2, 1-3, and 1-4 pairs that are connected through bonds, will have their non-bonded interactions scaled to 0.0. so if not using fix shake, but harmonic bonds the bonds will remain in rest, if the distances between the atoms is at the location of the potential energy minimum. if you still want the coulomb interactions be considered, you need to change the scaling factors for coulomb interactions to 1.0. however, for fix shake, those bond forces will cancel out due to the constraint forces and you still wont see any motion because of issue 1)
this is all straightforward and common behavior of classical MD force field codes.