Differences

This shows you the differences between two versions of the page.

--- exercise:mm_uzh:index [2014/05/23 11:19] – [Week 3] talirz
+++ exercises:2014_uzh_molsim:index [2014/10/15 14:24] – talirz
@@ Line 1: / Line 1: @@
 ====== Molecular Simulations ======
-The following exercises are part of the the course [[http://www.vorlesungen.uzh.ch/FS13/suche/sm-50018861.modveranst.html|Molecular simulations]] held at the University of Zurich during the spring semester 2014.
+The following exercises are part of the the course [[http://www.vorlesungen.uzh.ch/FS13/suche/sm-50018861.modveranst.html|Molecular simulations]] held by [[http://www.pci.uzh.ch/iannuzzi/|Marcella Iannuzzi]] at the University of Zurich during the spring semester 2014.
 ===== Introduction =====
@@ Line 7: / Line 7: @@
 Getting familiar with the command line, Gnuplot and VMD.
-  - [[exercise:mm_uzh:bash_terminal|The bash terminal in MacOS X]]
+  - [[bash_terminal|The bash terminal in MacOS X]]
-  - [[exercise:mm_uzh:gnuplot|2d plotting with Gnuplot]]
+  - [[gnuplot|2d plotting with Gnuplot]]
-  - [[exercise:mm_uzh:vmd|3d visualization with VMD]]
+  - [[vmd|3d visualization with VMD]]
-  - [[exercise:mm_uzh:ssh|Working on remote computers with SSH (optional)]]
+  - [[ssh|Working on remote computers with SSH (optional)]]
-|Required files | {{ :exercise:mm_uzh:intro.tar?direct&400 |}}|
+|Required files | {{ intro.tar?direct&400 |}}|
 ===== Week 1 =====
@@ Line 18: / Line 18: @@
 Ingredients of a force field and molecular dynamics in action.
-  - [[exercise:mm_uzh:h2o_ff|Constructing a force field for the $\text{H}_2\text{O}$ molecule]]
+  - [[h2o_ff|Constructing a force field for the $\text{H}_2\text{O}$ molecule]]
-  - [[exercise:mm_uzh:h2o_md|Molecular dynamics of liquid $\text{H}_2\text{O}$]]
+  - [[h2o_md|Molecular dynamics of liquid $\text{H}_2\text{O}$]]
-|Required files | {{ :exercise:mm_uzh:week1.tar?direct&400 |}}|
+|Required files | {{ week1.tar?direct&400 |}}|
 ===== Week 2 =====
@@ Line 27: / Line 27: @@
 Sampling dynamical properties, dealing with surfaces of crystals and a glimpse of QM/MM.
-  - [[exercise:mm_uzh:h2o_diff|Diffusion constant, viscosity and size effects]]
+  - [[h2o_diff|Diffusion constant, viscosity and size effects]]
-  - [[exercise:mm_uzh:chp_cu111|QM/MM: Cyclohexaphenylene on Cu(111)]]
+  - [[chp_cu111|QM/MM: Cyclohexaphenylene on Cu(111)]]
-|Required files | {{ :exercise:mm_uzh:week2.tar?direct&400 |}}|
+|Required files | {{ week2.tar?direct&400 |}}|
 ===== Week 3 =====
@@ Line 36: / Line 36: @@
 The 'chemical reaction' of $\text{NaCl}$ dissociating into $\text{Na}^+$ and $\text{Cl}^-$ in an aqueous environment and an example of a two-dimensional potential energy surface.
-  - [[exercise:mm_uzh:nacl_md|Free and constrained molecular dynamics]]
+  - [[nacl_md|Free and constrained molecular dynamics]]
-  - [[exercise:mm_uzh:nacl_free_energy|Profiles of potential energy and free energy]]
+  - [[nacl_free_energy|Profiles of potential energy and free energy]]
-  - [[exercise:mm_uzh:alanine_dipeptide|Potential energy surface of Alanine dipeptide]]
+  - [[alanine_dipeptide|Potential energy surface of Alanine dipeptide]]
-|Required files | {{ :exercise:mm_uzh:week3.tar?direct&400 |}}|
+|Required files | {{ week3.tar?direct&400 |}}|