How can I define a flexible molecules in a def file such that bond length between 0-3 is a function of bond lengths of 0-1 and 0-2 and the angle between 0-1-2? (d3 = d1cos(theta) + d2cos(theta)).
How can we use functions in .def file? And being a flexible model, this length should change every timestep, but since the .def file is only read at the start of this simulation, is there any other way to define this molecule?