https://www.cp2k.org/ 2026-05-04T19:38:26+00:00 https://www.cp2k.org/ https://www.cp2k.org/_media/wiki:logo.png text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2020_uzh_acpc2:ex01?rev=1598004913&do=diff Lennard-Jones liquids In this exercise, you will simulate a fluid of monoatomic particles that interact with a Lennard-Jones potential. The method to be used is molecular dynamics (MD) with periodic boundary conditions using CP2K. The aim is to explore the method, calculate the radial distribution function $g(r)$$U(x)=4\epsilon \left [\left ( \frac{\sigma }{r_{ij}} \right )^{12}- \left ( \frac{\sigma }{r_{ij}} \right )^{6} \right ]$$\epsilon$$g(r)$$\rho$$\sigma$$\epsilon$$r$$\epsilon$$\sigma$$… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2020_uzh_acpc2:ex02?rev=1598004913&do=diff Molecular Solution Water Water molecular models are computational techniques that have been developed in order to help discover the structure of water. In this section, you will be asked to calculate some physical properties based on classical molecular dynamics simulation. The TIP3/Fw model will be usded in the simulations. $g(r)$$r$$g(r)$$g_{O-O}(r)$\begin{equation} A(\omega)\propto{\int\langle{\dot{\mu}}({\tau}){\dot{\mu}}(t+{\tau})\rangle_{\tau}e^{-i{\omega}t}d{t}}, \label{eq:auto} \end{eq… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2020_uzh_acpc2:ex03?rev=1598004913&do=diff Nudged elastic band and free energy calculations In this exercise we will study the $S_N2$ nucleophilic substitution reaction $$ \text{Cl}^- + \text{CH}_3\text{Cl} \longleftrightarrow \text{Cl}\text{CH}_3 + \text{Cl}^-. $$ For energy and force evaluation, we will use the Parameterization Method 6 (PM6), which is a relatively inexpensive semiempirical model for electronic structure evaluation. For accurate reaction characterizations, ab initio methods, such as $3N$$S_N2$$$ F(s) = -k T \log(P(… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2020_uzh_acpc2:index?rev=1598004913&do=diff Exercises The following exercises are part of the course Advanced concepts of Physical Chemistry II: Statistical Mechanics and Molecular Simulations held at University Zürich during the spring semester 2020. Please send the report in PDF format to the teaching assistant before the deadline. Exercise 0 login local cluster TCOPT2 cp2k calculation and visulization Exercise 1 Lennard-Jones liquids Deadline: 28th April 2020 text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2020_uzh_acpc2:installation?rev=1598004913&do=diff First CP2K simulation Module loading Since there are numerous applications with different and possibly conflicting requirements, the module system is used. This means that only basic commands are available until explicitly loaded. To list all available modules: text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2020_uzh_acpc2:login?rev=1598004913&do=diff First Login In this exercise you will learn how to login and run commands on our infrastructure. Part I: Login Required software As mentioned in the lecture, you absolutely need a terminal emulator: * on Linux: this can be one of programs Konsole, Gnome Terminal, Terminal, XTerm,