Messages

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?

I am not sure if this question is relevant here, but I have a very basic doubt. I have a .cif file of a crystal, it has _atom_site_disorder_group and _atom_site_disorder_assembly for some of the atoms. I understand that it means there are multiple sites for those atoms possible with similar potential energy. But to use the structure in any computation, we have to assign some position and connectivity to those atoms. How can we do that? Is there any standard method to deal with such disorder?