The multi-frame model was prepared by Angel Herráez from molecular dynamics data kindly provided by Luboš Vrbka[1] (Institute of Organic Chemistry and Biochemistry, Prague). Dr. Vrbka's data were converted from Gromacs .gro to pdb format using the editconf program[2], then existing dummy atoms for electron centers were removed and everything was collated into a single multi-frame pdb file. Frames 1 to 40 correspond to time points 70 to 109 seconds from a representative trajectory of freezing simulation.
In this page, the model is shown using Jmol capabilities. Covalent bonds are automatically determined by Jmol, while hydrogen bonds are generated between those oxygen and hydrogen atoms that are not covalently bonded and are separated by a distance below the value specified above.
Water and ice images are from Wikimedia Commons, under GNU Free Documentation License version 1.2 or any later version.
