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exercises:2015_uzh_molsim:vmd [2015/04/23 12:20]
exercises:2015_uzh_molsim:vmd [2020/08/21 10:15] (current)
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 +====== 3d visualization with VMD ======
  
 +[[http://www.ks.uiuc.edu/Research/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 [[http://www.ks.uiuc.edu/Research/vmd/current/ug/node15.html|VMD tutorial]].
 +
 +Starting VMD
 +<code bash>
 +vmd                  # start vmd
 +vmd pos.xyz          # start vmd and load position file 'pos.xyz'
 +vmd -e view.vmd      # start vmd and load previously saved visualization state 'view.vmd'
 +</code>
 +
 +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
 +  * //Plot a specific bond length versus frame number//: Graphics -> Labels -> Bonds -> Graph
 +  * //Render the current view as bitmap image// (''.bmp''): File -> Render.. -> Snapshot.  
 +  * //Note//: Click 'Browse' to place the ''.bmp'' in the desired directory.
 +
 +
 +     
 +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**
 +
 +  - From the [[http://www.rcsb.org/pdb/home/home.do|RCSB Protein Data Bank]] download the PDB file for rubredoxin. We will use the structure determined by Watenpaugh et al. with PDB ID ''4RXN''.
 +  - Visualize the protein with VMD. Suggestion: Draw the backbone with NewCartoon and color it according to the secondary structure.
 +  - Find the $\text{FeS}_4$ active site and measure the 4 $\text{Fe}-\text{S}$ distances.
 +  - Render a snapshot of the active site with the measured distances.
 +</note>
 +
 +Now we are ready to analyze a molecular dynamics trajectory.
 +The file ''nacl.xyz'' in the ''intro'' folder contains the trajectory of a MD simulation of $\text{NaCl}$ in water, which naturally was performed under periodic boundary conditions.
 +
 +For simulations with periodic boundary conditions it is often helpful to draw the simulation box.
 +In VMD this is achieved by typing the following (for a cubic simulation cell with 10 angstroms side length) on the terminal
 +<code>
 +pbc set {10 10 10} -all
 +pbc box
 +</code>
 +
 +<note>**TASK 2**
 +
 +  - How many water molecules were simulated?
 +  - Visualize the trajectory with VMD. You may want to change the representation style from 'lines' to something else.
 +  - 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 side length 12.4138 Angstroms and periodic boundary conditions. Draw the simulation box.
 +  - 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>