https://www.cp2k.org/ 2026-05-06T09:30:16+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:2018_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 2018. Exercise 0 cp2k installation and shell environments Exercise 1 * Lennard-Jones liquids Exercise 2 * Molecular solutions Exercise 3 * Protein Folding in Solution text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2018_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:2018_uzh_acpc2:l-j_flu?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$$g(r)$$\epsilon$$\sigma$$\epsilon$$\sigma$$g(r)$$g(r… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2018_uzh_acpc2:mol_sol?rev=1598004913&do=diff Molecular Solution Water Water molecular models are computational techniques that have been developed in order to help discover the structure of water. In this section, you will be asked to calculate some physical properties based on classical molecular dynamics simulation. The TIP3/Fw model will be usded in the simulations. $g(r)$$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:2018_uzh_acpc2:prot_fol?rev=1598004913&do=diff Protein Folding in Solution In this exercise, you will calculate the protein folding free energy using thermodynamic integration, a method based on molecular dynamics (MD). The protein will be described by the empirical force field, CHARMM22, <http://mackerell.umaryland.edu/charmm_ff.shtml> Background $F(x)$\begin{equation} \Delta A = -\int_a^b F(x)\, dx \end{equation}$a$$b$$14.37$$F(x)$$x$$F(x)$$a$$b$\begin{equation} \Delta A = -\int_a^b F(x)\, dx \end{equation}$x^\prime$$x^\prime$\begin{equa…