https://www.cp2k.org/ 2026-05-04T15:52:31+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:2014_uzh_molsim:alanine_dipeptide?rev=1598004913&do=diff Potential energy surface of alanine dipeptide Alanine dipeptide 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$$\psi$ text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_uzh_molsim:bash_terminal?rev=1598004913&do=diff The bash terminal in MacOS X Many tasks in the following weeks will need to be performed on the terminal (or 'command line'). Hit CMD + SPACE to open the search window, enter 'terminal' and hit RETURN. -> Let's continue with a list of useful commands text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_uzh_molsim:chp_cu111?rev=1598004913&do=diff QM/MM: Cyclohexaphenylene on Cu(111) Systems containing thousand atoms and more (e.g. polymers, reactions in solution, molecules on surfaces) are hard to describe fully ab initio. In many applications, however, the main attention focusses on a small subset $E(N)$$N$$\triangle E(N) = E(N) − E(N − 1)$$\triangle E(\infty)$$\sigma$$$\sigma =\lim_{N\rightarrow\infty} \frac{1}{2} \frac{1}{A} (E(N)−N \triangle E(N))$$$A$$\triangle E(N)$$N$$\sigma$$1\,\text{erg} = 10^{-7}\,\text{J}$$T_m$$T_m$$T_m$$l_z$… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_uzh_molsim:gnuplot?rev=1598004913&do=diff 2d plotting with Gnuplot Gnuplot is a command-line driven graphing utility that is available for many different operating systems. Gnuplot is a powerful program that can be used to generate publication-quality figures. Here, we are going to introduce only a small subset of its features. If you are interested to learn more, have a look to the $x$$f(x)$$f(x)=ax^2$ text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_uzh_molsim:h2o_diff?rev=1598004913&do=diff Diffusion constant, viscosity and size effects When simulating liquids or solids under periodic boundary conditions, we are making two fundamental approximations: * We simulate an infinite system, thus neglecting the fact that any real-world system is finite. This approximation becomes problematic, when the real-world system to be studied consists only of a few simulation cells.$T=300\,\text{K}$$D_{pbc}(L)$$L$$D=\lim\limits_{L\rightarrow \infty}D_{pbc}(L)$$NVT$$$\text{msd}(t) = \langle |r(t+… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_uzh_molsim:h2o_ff?rev=1598004913&do=diff Constructing a force field for the $\text{H}_2\text{O}$ molecule In this exercise, we are going to construct a force field for the $\text{H}_2\text{O}$ molecule by fitting the parameters of the water model used in 10.1063/1.1884609 to ab initio calculations of the $\text{H}_2\text{O}$ molecule. TASK 1 $\text{H}_2\text{O}$$\text{H}_2\text{O}$ text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_uzh_molsim:h2o_md?rev=1598004913&do=diff Molecular dynamics of liquid $\text{H}_2\text{O}$ Radial distribution function We have prepared a CP2K input file md.in for running a MD simulation of liquid water using the force field from the first exercise (parametrized by Praprotnik et al.). TASK 1$g(r)$$g(r)$$g_{O-O}(r)$$\text{H}_2\text{O}$ text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_uzh_molsim:index?rev=1598004913&do=diff Molecular Simulations The following exercises are part of the the course Molecular simulations held by Marcella Iannuzzi at the University of Zurich during the spring semester 2014. Introduction Getting familiar with the command line, Gnuplot and VMD. * The bash terminal in MacOS X * 2d plotting with Gnuplot * 3d visualization with VMD * Working on remote computers with SSH (optional) Required files $\text{NaCl}$$\text{Na}^+$$\text{Cl}^-$ text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_uzh_molsim:nacl_free_energy?rev=1598004913&do=diff Profiles of potential energy and free energy We are going to start with the simplified example of isolated $\text{Na}^+$ and $\text{Cl}^-$ in the gas phase, where we can directly compare the results of our computer simulation against the analytical formulae used to describe the interaction potential.$\text{Na}^+$$\text{Cl}^-$$T=1\,\text{K}$$1\,\text{K}$$g(r)$$F(r)$$$\begin{eqnarray} g(r)4\pi r^2 &\propto& \int \delta(r-r') \exp(-\beta H(r'))\,dr \\ P(r) &\propto& \int \delta(r-r') \exp(-\beta… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_uzh_molsim:nacl_md?rev=1598004913&do=diff Free and constrained molecular dynamics We have prepared an input file free.in to perform an unconstrained molecular dynamics of $\text{NaCl}$ dissolved in water. TASK 1 * Look inside free.in, report which interactions are considered and how they are modeled. Can you write down the Hamiltonian? $\text{NaCl}$$\text{NaCl}$$\text{NaCl}$$\text{Na}$$\text{Cl}$$\text{NaCl}$$\unicode{x212B}$$\unicode{x212B}$$n_1$$\unicode{x212B}$ text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_uzh_molsim:ssh?rev=1598004913&do=diff Working on remote computers with SSH The Secure Shell network protocol allows you to connect to remote computers through a an encrypted channel. SSH is the standard tool used by computational scientists to interact with computer clusters and supercomputers around the world. text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_uzh_molsim:vmd?rev=1598004913&do=diff 3d visualization with VMD Visual Molecular Dynamics can display, animate, and analyze large biomolecular systems using 3-D graphics and built-in scripting. Again, we are going to use only a small subset of VMD's powers here. You are very welcome to dig deeper in the nice VMD tutorial.$\text{FeS}_4$$\text{Fe}-\text{S}$$\text{NaCl}$$\text{Na-Cl}$