2 questions related to periodicity in 1 or 2 dimensions:
I tried a lattice minimization (based on the test case) on a crystal structure of a polymer, using image patching across the boundary of the unit cell. The ABNR minimization exited before reaching the maximum nstep, and the first derivative was unchanged for any of the atoms (far from zero). Does lattice minimization not work with image patching, or am I missing something?
Also, I've come across some papers that derive Ewald summation methods for systems that are periodic in 2 dimensions (such as a solid surface or membrane) or periodic in 1 dimension (a pore or channel). Both of these papers state that the "usual" 3D Ewald is not appropriate for this type of periodicity, but do not explain why it does not work. Applying 3D crystal symmetry leads to lamellar stacking of surfaces or parallel helices or pores - and I believe this is the only way CHARMM can handle these types of periodicity using Ewald electrostatics. Can someone with a better understanding explain why this is inappropriate when using 3D Ewald, or alternatively why these authors are overstating their claims?
M. Kawata et al J. Chem. Phys. 116 (8) 3430-3448 February 2002
A. Brodka Chem. Phys. Letters 363 604-609 September 2002