problem in clustering MDS when the protein moves out from one edge of water box while applying periodic boundary conditions about ttclust

[tubiana]

Hi!

TTClust only perform the clustering, all the "cleaning" has to be done prior to TTClust execution.
For example, I usually clean my trajectories by removing the waters, making the molecule whole again and aligning the protein on itself through the trajectory.
If you used Gromacs it is the "trjconv" tools.
If you want more details, you can check my Gromacs tutorial (part 4.2) http://tubiana.me/teaching_files/biocat2020/Tutorial_Gromacs-2019.pdf
Best regards,
Thibault.

[hima111997]

Thanks I use vmd to fix the structure then clustered and it worked Sent from Yahoo Mail on Android On الأحد, مارس ٢١, ٢٠٢١ at ٢:٠٢ م, Thibault ***@***.***> wrote: Hi! TTClust only perform the clustering, all the "cleaning" has to be done prior to TTClust execution. For example, I usually clean my trajectories by removing the waters, making the molecule whole again and aligning the protein on itself through the trajectory. If you used Gromacs it is the "trjconv" tools. If you want more details, you can check my Gromacs tutorial (part 4.2) http://tubiana.me/teaching_files/biocat2020/Tutorial_Gromacs-2019.pdf Best regards, Thibault. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.