Hello, everyone..I got the same issue as I begun a MD it finished and then got to "Not responding mode", but I understand and still waiting for it to finish. I got VMD/Namd2 for MD, yet I do really enjoy the graphics and analysis interface of Chimera. Question is Can I run MD in VMD/Namd2 and do analysis on Chimera? How can I import MD data from VMD into Chimera? Thanks.
Yes, you can: Chimera > Tools > MD/Ensemble Analysis > MD Movie > Trajectory Format NAMD (PSF/DCD).
PS: I wouldn't recommend it. VMD is much more efficient than Chimera for handling large trajectories.
@Mustafa Tekpinar...thank you ...I was quite impressed by Chimera cluster analysis. It can devem provide am average structure of a ficam cluster. Is there any similar in VMD?
You are welcome. I don't remember a clustering algorithm implemented directly in VMD. I used https://github.com/tubiana/TTClust and 'gmx cluster' recently for that purpose. VMD can still serve you for converting your dcd trajectory to trr or xtc formats.
- Badges
- Science topic
- Similar topics
- Analytical Chemistry
- Extraction