Differences

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--- exercise:mm_uzh:vmd [2014/04/24 17:16] – talirz
+++ exercise:2014_uzh_molsim:vmd [2014/10/15 13:44] – oschuett
@@ Line 12: / Line 12: @@
 </code>
-Some additional useful commands
+VMD **does** have a graphical user interface (yay!), although knowing how to use the scripting console is also advisable.
+Some common tasks are:
   * //Edit representation of structure//: Graphics -> Representations
   * //Measure distance between atoms//: Mouse -> Label -> Bonds
@@ Line 21: / Line 22: @@
-We are going to start by creating a visual representation of the protein 'rubredoxin'.
+We are going to start by creating a visual representation of the protein rubredoxin.
+{{ rubredoxin.png?direct&400 |Representation of rubredoxin's secondary structure and active site generated by VMD.}}
 <note>**TASK 1**
@@ Line 43: / Line 45: @@
   - How many water molecules were simulated?
-  - Visualize the trajectory with VMD. You may want to change the representation style from lines to something else.
+  - Visualize the trajectory with VMD. You may want to change the representation style from 'lines' to something else.
-  - Measure the Na-Cl distance and create a plot of its evolution with the frame number.
+  - Measure the $\text{Na-Cl}$ distance and create a plot of its evolution with the frame number.
-  - The simulation was performed in a cubic box with sidelength 12.4138 Angstroms and periodic boundary conditions. Draw the simulation box.
+  - The simulation was performed in a cubic box with side length 12.4138 Angstroms and periodic boundary conditions. Draw the simulation box.
-  - Compare with the premade visualization state nacl.vmd. What is different here?
   - In the course of the simulation, the molecules start moving outside of the box! Does this indicate a problem?
+  - Compare with the premade visualization state ''nacl.vmd''. Describe the mathematical transformation that has been applied here.
 </note>