I am trying to learn how to do simulations of linear molecules consisting of 3 atoms by first simulating just a single
molecule. I am having two different problems.
1. using only [ fix shake ], when the 3 atoms are aligned linearly, the pressure is NAN. When I shift the positions of the
atoms such that they are not exactly linear, then I get numbers for both thermo properties and the SHAKE stats.
2. For a set of not exactly linear atoms, when I use [ fix shake ] and [ fix nve ] or [ fix nvt ], the 0th timestep is fine (I get numbers), but the afterwards I get NAN for thermo properties and SHAKE stats.
I have tried these simulations with no interactions between atoms via pair_coeff and neigh_modify exclude and still things misbehave when the molecule is exactly linear.
Below is the input file and the data file. I appreciate any advice. Thanks!