ps5_solution - (Similar to Fig. 1b in Ref.) The images in...

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10.675 Assignment #5 due 11/23/04 In this problem set, you will use CPMD to study the dynamics of a proton transferring among water molecules (H 9 O 4 + ). And you can compare what you observe with the literature report (Ref: Nature, vol. 397 , 1999, 601). Solution: The detailed procedure has been described in the problem statement. Here in the solution, we will only present the snapshots from the simulations (5000 steps). [Left: DynamicBond; Right: Hydrogen Bond] Snapshot 1 (Frame 1): H 9 O 4 + has an H 3 O + core that donates three hydrogen bonds to its neighboring H 2 O molecules. (Similar to Fig. 1a in Ref.) Snapshot 2 (Frame 141): One of the three protons of the H 3 O + core migrates along its hydrogen bond and forms an H 5 O 2 + , in which this proton is equally share between two water molecules.
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Unformatted text preview: (Similar to Fig. 1b in Ref.) The images in this solutions file were made with VMD/NAMD/BioCoRE/JMV/other software support. VMD/NAMD/BioCoRE/JMV/ is developed with NIH support by the Theoretical and Computational Biophysics group at the Beckman Institute, University of Illinois at Urbana-Champaign. Courtesy of the Theoretical and Computational Biophysics group at the Beckman Institute, University of Illinois at Urbana-Champaign. Used with permission. Snapshot 3 (Frame 335): H 9 O 4 + formed again. And three are three hydrogen bonds in the system again. Snapshot 4 (Frame 434): Further migration of a different proton in H 3 O + forms another H 5 O 2 + with one hydrogen bond. (Similar to Fig. 1d in Ref.)...
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ps5_solution - (Similar to Fig. 1b in Ref.) The images in...

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