exercises:2017_uzh_acpc2:mol_sol
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exercises:2017_uzh_acpc2:mol_sol [2017/05/04 15:02] – [Water] jglan | exercises:2017_uzh_acpc2:mol_sol [2017/05/17 13:23] – jglan | ||
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- | ====== | + | ====== |
===== Ramachandran plot ===== | ===== Ramachandran plot ===== | ||
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In particular, it has more than one long-lived conformation, | In particular, it has more than one long-lived conformation, | ||
- | The conformations of alanine | + | The conformations of glyala |
Below, we color carbons in green, hydrogens in white, oxygen in red and nitrogen in blue, i.e. | Below, we color carbons in green, hydrogens in white, oxygen in red and nitrogen in blue, i.e. | ||
the torsional angle $\phi$ is N-C-C-N , while $\psi$ is C-N-C-C along the backbone. | the torsional angle $\phi$ is N-C-C-N , while $\psi$ is C-N-C-C along the backbone. | ||
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- The atomic indices defining the dihedral indices in the input file '' | - The atomic indices defining the dihedral indices in the input file '' | ||
- Use '' | - Use '' | ||
- | - Use gnuplot to plot the potential energy surface (we have provided a script '' | + | - Use gnuplot to plot the potential energy surface (we have provided a script '' |
</ | </ | ||
===== Water ===== | ===== Water ===== | ||
- | We have prepared a CP2K input file '' | + | We have prepared a CP2K input file '' |
Repeat the MD using initial temperatures 200 and 400 K. In order not to overwrite any of your previous files, it is advisable to run the new simulations in different folders. | Repeat the MD using initial temperatures 200 and 400 K. In order not to overwrite any of your previous files, it is advisable to run the new simulations in different folders. |
exercises/2017_uzh_acpc2/mol_sol.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1