exercises:2014_uzh_molsim:vmd
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| Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
| exercise:mm_uzh:vmd [2014/04/24 17:25] – talirz | exercise:mm_uzh:vmd [2014/04/28 17:37] – added rubredoxin pic talirz | ||
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| 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. | ||
| + | {{ : | ||
| < | < | ||
| Line 44: | Line 45: | ||
| - How many water molecules were simulated? | - 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' |
| - | - 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 | + | - The simulation was performed in a cubic box with side length |
| - In the course of the simulation, the molecules start moving outside of the box! Does this indicate a problem? | - 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. | + | - Compare with the premade visualization state '' |
| </ | </ | ||
exercises/2014_uzh_molsim/vmd.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1