I have imported a MD trajectory in VMD. I need to generate plots like how the distance between two selected atoms is changing over the simulation. Is there a way to do this in VMD?
Thanks.
Yes, there is a way to do what you want. You have to familiarise yourself with VMD. Please use the following link to help yourself.
https://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node7.html
I would recommend you to use Xmgrace if you want to plot your data. Xmgrace is easy to learn and very much user friendly. Heaps of tutorials are available.
Of course, there are a number of things VMD can do.
For instance, you can perform RMSD alignments, calculate distance between groups, generate movies from trajectories....
Yes you can. You have to use the level option of VMD. First Choose the Mouse > Label > Bonds, and then select the atoms that you want to measure the distance.
Once you selected, go to the graphics option, then change atom option to bonds, then select Graph.
Hope this might help you
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