Large differences in gmx mindist values with and without PBC correction

User discussions
1

Dear users,
I simulated a protein for 1 µs and calculated the minimum distance using:

gmx mindist -s .tpr -f .xtc -od mindist.xvg -n .ndx

I computed mindist on the raw trajectory and again after applying PBC corrections, but the results differ substantially. As far as I understand, mindist should be the same after GROMACS’ automatic corrections. Can anyone help me understand why I see such large differences?

Thanks

Devid

2

What do you mean with “after applying PBC corrections”?

gmx mindist should always produce correct distances.

3

Hii @hess

Thanks for your reply.

I mean that I calculated the mindist using two trajectory (.xtc) files:

  1. The raw trajectory resulted from the MD simulation and
  2. The trajectory after centering the protein and fitting the backbone

and I am getting different results in the two cases.

4

Fitting rotates the structure, then the trajectory is no longer compatible with the box.

5

I also tested the centered trajectory (.xtc) without fitting, but the results are still different compared to the raw trajectory from the MD simulation.

6

That is strange. Translated doesn’t affect distances.