How to get the wnrapped trajectory file?

User discussions
1

Dear Gromacs users:

I want to write a code to calculate MSD using Gromacs trajectory. I changed the trajectory file to the text file using gmx dump. However, I figured out the trajectory is in the wrapped form which does not show the real trajectory of the diffusant outside of the box. I need the real distance traversed by the atoms.

What should I do to get the unwrapped trajectory file?

Thanks

2

Do you mean gmx trjconv -pbc nojump?

3

Thanks for your reply,

but it just shows the movement in just positive direction. I mean the molecules cross the box from just 3 dimensions of the cube. (x,y and z) instead of (x,y,z,-x,-y,-z)

4

I don’t understand what you mean.

5

Dear MagnusL,

Sorry for the late response. As you can see the water molecules are going out of the box in 3 directions. Indeed, we expect for 6 directions. The pink structure is Zeolite and blue is water.

Thanks

Screenshot from 2024-10-14 12-54-21
Screenshot from 2024-10-14 12-54-211279×862 144 KB

6

That looks strange indeed. Would you be able to share the xtc file somewhere, and preferably also confout.gro from the simulation?

7

Thanks for your reply.

I don’t know how I can share my .xtc file. Do you have any suggestions?

Thanks

8

Dear MagnusL

I found the main problem. -pbc nojump is working correctly.

Thanks a lot.

9

Great to hear!