Hi all,
The system that I am going to simulate consists of liquid crystal
molecules in contact with a polymer surface. My problem is that when I
run (NVT) simulations from different starting configurations, the
average potential energies (after equilibration) are different, and
this difference is mostly due to difference in bond energies. If the
difference were due to difference in non-bond energies, it would be
understandable, but I do not see how bond energy can depend on initial
configuration (in this case initial orientation of liquid crystal
molecules). I suspect something is wrong. Can anybody help me with this
one?
Thanks a lot,
Mehdi