exercises:2021_uzh_acpc2:installation
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exercises:2021_uzh_acpc2:installation [2021/04/13 13:21] – Update instructions mrossmannek | exercises:2021_uzh_acpc2:installation [2021/04/14 12:30] (current) – [Part II: Loading and running a program] Update VMD instructions mrossmannek | ||
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- | === Using VMD === | + | === Getting the input data === |
- | Now, we are ready to visualize the previously computed trajectory | + | Before you can try out VMD, we must get some data to visualize. |
+ | For now, we simply want to view all the Argon atoms from our previous simulation. | ||
+ | To do so, we need to extract their coordinates from the input file. | ||
+ | The easiest solution to this, is to copy them into an [[https:// | ||
+ | < | ||
+ | cp argon.inp argon.xyz | ||
+ | </ | ||
+ | Now, you must remove everything but the atoms coordinates. | ||
+ | You should end up with 108 lines in your file, each containing the coordinate of a single Ar atom. | ||
- | <note todo> | + | To make this a fully functional '' |
+ | - The number of atoms on the first line | ||
+ | - A blank line (or a comment) | ||
+ | - The rest of the file | ||
+ | < | ||
+ | 108 | ||
+ | |||
+ | Ar -8.53869012951987116 -15.5816257770688615 2.85663672298278293 | ||
+ | ... | ||
+ | </code> | ||
+ | |||
+ | === Using VMD === | ||
+ | |||
+ | Now, we are ready for our first visualization with VMD. | ||
Open VMD. From '' | Open VMD. From '' | ||
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</ | </ | ||
- | A snapshot of the molecular dynamics trajectory should approximately look like this: | + | <note tip>'' |
- | {{:exercises: | + | <note tip> |
+ | If you prefer to load the file and set the drawing methods via commands, you can do the following: | ||
+ | < | ||
+ | mol new argon.xyz | ||
+ | mol modstyle 0 0 vdw | ||
+ | </ | ||
+ | The first commands loads the file '' | ||
+ | The second command assumes this is the first file you load (the first index '' | ||
+ | </ | ||
+ | A snapshot of the molecular dynamics trajectory should approximately look like this: | ||
+ | {{: | ||
===== Plotting tools ===== | ===== Plotting tools ===== |
exercises/2021_uzh_acpc2/installation.1618320062.txt.gz · Last modified: 2021/04/13 13:21 by mrossmannek