https://www.cp2k.org/ 2026-04-13T22:48:36+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:2017_uzh_acpc2:faq?rev=1598004913&do=diff First Login In this exercise you will learn how to login and run commands on our infrastructure. Part I: Login As mentioned in the lecture, you absolutely need * a X11-Server: * on Linux: it is enough to be logged-in in a graphical environment (Unity, Gnome, KDE, text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_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 2017. Login and running commands 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:2017_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$$g(r)$$\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:2017_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 As mentioned in the lecture, you absolutely need * a X11-Server: * on Linux: it is enough to be logged-in in a graphical environment (Unity, Gnome, KDE, text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_uzh_acpc2:mol_sol?rev=1598004913&do=diff Molecular Solution Ramachandran plot Glyala is one of the simplest molecules that exhibits some important features common to larger biomolecules. In particular, it has more than one long-lived conformation, which we will identify in this exercise by mapping out its $\phi$$\psi$$g(r)$$g(r)$$g_{O-O}(r)$ text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_uzh_acpc2:prot_fol?rev=1598004913&do=diff Protein Folding in Solution In this exercise, you will calculate the protein folding free energy in aqueous solution using thermodynamic integration, a method based on molecular dynamics (MD). The protein will be described by the empirical force field, $F(x)$\begin{equation} \Delta A = -\int_a^b F(x)\, dx \end{equation}$a$$b$$18.36$$15$$20 $$F(x)$$x$$\Delta A$