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Published 2 years ago • verified publisher icon tdudgeon

Separated complex in simulation results

Open ivandon15 opened this issue 1 year ago • 2 comments

Hi,

Have you ever encountered a situation in your simulation results where the protein's position remains roughly unchanged, but the ligand jumps from one side to the other (seemingly influenced by boundary conditions)? image

Besides that, there have also been instances where the ligand and the protein are very far apart, appearing to be unrelated to each other. (Figures depicted as below) image image

This really confuses me, and I also tried to set enforcePeriodicBox=True when outputting the traj.

Thanks for your contributions! It really helps me a lot.

ivandon15 avatar Jun 18 '24 02:06 ivandon15

Yes, this looks like a periodic boundary issue. Did you try using the analyse.py script to re-image the trajectory?

tdudgeon avatar Jun 19 '24 07:06 tdudgeon

Thank you for replying! Yes, I do use analyse.py to reimage. And as mentioned before, I also tried enforcePeriodicBox=True, but it seems that none of them work. Besides, I think probably re-imaging is only changing the position of the entire complex but remain the relative position unchanged, right?

ivandon15 avatar Jun 19 '24 10:06 ivandon15