I have a system which is an aptamer binds to AMP and run for 10us. Since the aptamer is moving inside the PBC a lot, so I tried to wrap it with these commands:
Unfortunately, after I fit the trajectory with -fit rot+trans and visualize it in VMD, the PBC box is moving around the aptamer, so when I use +x and -x for PBC, it does not align. Could you please help me how should I wrap my system?
If I understand correctly you want to take a look at the PBC images after the full PBC clean-up procedure.
I think there is no way around this. Or you stop before the -fit rot+trans step, so you stay in the box reference frame, and so you can correctly represent the PBC images of your molecules, or you fit to a frame, and so you “move” your reference frame to the molecule, but in that case the box itself will rotate around the fitted molecule, and so will the PBC images. I would honestly visualize the trajectory before the fitting procedure if I wanted to check PBC and after if I wanted to check the molecule behaviour.
Thank you so much for your suggestion. I stopped at the step before -fit rot+trans, and the PBC stopped moving, which is exactly what I want. However, I am not sure whether I need to include the -fit step, because if I stop at the center+compact step, the RNA moves more than when I include -fit as the box is moving along the RNA.
This is really up to you. The output of the simulation doesn’t (and shouldn’t) change with a clean up of the trajectory. So if you are worried about quantities like RMSD, RMSF, distances etc these are independent from any fitting. Personally, the rot+trans refitting is something useful when visualising complex trajectoriers, but I would be aware that a rotating box might cause issues with some tools.