exercises:2015_uzh_molsim:vmd
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— | exercises:2015_uzh_molsim:vmd [2020/08/21 10:15] (current) – created - external edit 127.0.0.1 | ||
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+ | ====== 3d visualization with VMD ====== | ||
+ | [[http:// | ||
+ | |||
+ | 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:// | ||
+ | |||
+ | Starting VMD | ||
+ | <code bash> | ||
+ | vmd # start vmd | ||
+ | vmd pos.xyz | ||
+ | vmd -e view.vmd | ||
+ | </ | ||
+ | |||
+ | 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//: | ||
+ | * //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// ('' | ||
+ | * //Note//: Click ' | ||
+ | |||
+ | |||
+ | |||
+ | We are going to start by creating a visual representation of the protein rubredoxin. | ||
+ | {{ rubredoxin.png? | ||
+ | < | ||
+ | |||
+ | - From the [[http:// | ||
+ | - 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. | ||
+ | </ | ||
+ | |||
+ | Now we are ready to analyze a molecular dynamics trajectory. | ||
+ | The file '' | ||
+ | |||
+ | 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 | ||
+ | < | ||
+ | pbc set {10 10 10} -all | ||
+ | pbc box | ||
+ | </ | ||
+ | |||
+ | < | ||
+ | |||
+ | - How many water molecules were simulated? | ||
+ | - Visualize the trajectory with VMD. You may want to change the representation style from ' | ||
+ | - 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 '' | ||
+ | </ |