https://www.cp2k.org/ 2026-05-06T13:29:49+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:2019_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:2019_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)$$g_{O-O}(r)$\begin{equation} A(\omega)\propto{\int\langle{\mu}({\tau}){\mu}(t+{\tau})\rangle_{\tau}e^{-i{\omega}t}d{t}}, \label{eq:auto} \end{equation}\begi… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2019_uzh_acpc2:ex03?rev=1598004913&do=diff Nudged elastic band and free energy calculations In this exercise we will study the $S_N2$ nucleophilic substitution reaction $$ \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:2019_uzh_acpc2:index?rev=1598004913&do=diff Exercises The following exercises are part of the the course Advanced concepts of Physical Chemistry II: Statistical Mechanics and Molecular Simulations held at University Zürich during the spring semester 2019. Exercise 0 cp2k installation and shell environments login local cluster TCOPT2 Exercise 1 Lennard-Jones liquids Exercise 2 Molecular Solutions Exercise 3 Nudged elastic band and free energy calculations text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2019_uzh_acpc2:installation?rev=1598004913&do=diff Exercise 0 In this exercise you will learn how to use the bash terminal, to do a minimal installation of CP2K, which will be used to perform the molecular dynamics simulations, and to install a few useful programs required to analyse the simulations. text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2019_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,