Electronic Thesis and Dissertation Repository


Master of Science


Applied Mathematics


Dr. Mikko Karttunen


We present classical molecular dynamics (MD) simulations providing insight into the behaviour of water. We focus on confined water, the properties of which are often significantly different from the properties of bulk water.

First, we performed several simulations investigating the handling of long-range interactions in GROMACS [1], a MD simulation package. Selection of simulation protocols such as handling of long-range interactions is often overlooked, sometimes to the significant detriment of the final result [2, 3, 4]. Ensuring that the chosen simulation protocols are appropriate is a critical step in computer simulation.

Second, we performed MD simulations where water flowed between two reservoirs con- nected by a carbon nanotube. We analyzed 10 simulations where two types of changes were made to induce flow: The removal of water molecules from one reservoir and the addition of NaCl to one reservoir at one of two concentrations. We study the effects of these changes in isolation, cooperation and competition.

[1] B Hess, C Kutzner, D van der Spoel, and E Lindahl. Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput., 4:435–447, 2008.

[2] D. J. Bonthuis, K. F. Rinne, K. Falk, C. N. Kaplan, D. Horinek, A. N. Berker, L. Bocquet, and R. R. Netz. Theory and simulations of water flow through carbon nanotubes: prospects and pitfalls. J. Phys.: Condens. Matter, 23:184110, 2011.

[3] J. Wong-ekkabut and M. Karttunen. Assessment of common simulation protocols for simulations of nanopores, membrane proteins, and channels. J. Chem. Theory Comput. DOI: 10.1021/ct3001359.

[4] J. Wong-ekkabut,M. S. Miettinen, C. Dias, and M. Karttunen. Static charges cannot drive a continuous flow of water molecules through a carbon nanotube. Nat. Nanotechnol., 5:555–557, 2010.