I need a way to rotate my entire system (DNA and solvent) such that the axis of the DNA lies along the x-axis, but I want the periodic boundaries to be preserved. I added pictures of my system before and after rotation.
How can I edit things in such a way that the entire system is rotated, but molecules stay within the box? (basically the water molecules that were rotated down and went outside the box should reappear up inside the box)
Thank you in advance!
This file must have some problem, and you need to generate fresh periodic boundary for your system (DNA-solvents).
Only you need to center your box on the desired molecule, in your gro and trajectory files (.gro and .trr or .xtc). This could be done with gmx trjconv, with the flag -center. You will be asked for a group of your index file to center your system. If your DNA is in both side of the box (I mean the periodic image), you need to choose only an atom or a group of atom, which were in the same side of the box during the whole trajectory, if not, the center of mass selected will jumping all over your trajectory from one side to another.
Regards
Florencia
Thank you very much for your responses!
Mohammad Mahdi Hajjari
editconf with the rotate flag still gives me a rotated system that has residues going out of the box, similar to the image I uploaded in my question. It did not preserve boundary conditions. Is there any other flag I should've added?Shaban Ahmad how do you generate fresh periodic boundaries? I tried to use the -pbc res and -pbc mol flags but it seems that's not the correct thing to do. I attached a snapshot of what I got.
M. Florencia Martini centering did help, but I'm still not sure how to deal with the periodic boundaries (the DNA is centered in the image I uploaded). Any help would be appreciated!
- Badges
- Science topic
- Similar topics
- Chemistry
- Theoretical Chemistry
- Computational Chemistry
- Molecular Dynamics