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Snapshot from an AMBER simulation of the C-terminal beta hairpin from protein G. The peptide was solvated with TIP3P water in a truncated octahedral box and counterions were added to bring the system to neutrality. The system was minimized and then equilibrated for 100 ps at 300K and 1 atm using Berendsen temperature and pressure control. Finally, a 50 ps NVE production simulation was conducted, with configurations saved every 0.1 ps, generating a trajectory of 500 snapshots. Data courtesy of John Chodera, Graduate Group in Biophysics, Dill group, UCSF.
Text was added with the 2D Labels tool in Chimera. Using a Chimera command script in MD Movie, hydrogen bonds were computed for each frame and only the water molecules forming hydrogen bonds with the peptide were displayed. Only the nonhydrogen atoms of the peptide are shown. The orange and aqua transparent blobs represent high-occupancy regions for water oxygen and hydrogen atoms, respectively, computed over the trajectory. Quicktime movie (~40 MB)