Fixing periodic boundary conditions distance artefacts

GROMACS version: 2019.2
GROMACS modification: No

Hi, I’ve got a system made up of hundreds of just one type of molecule (triacylgycerides) which are in the unit cell configuration (i.e. many stacked unit cells in 3D). The unit cell of this molecule is made up of 4 molecules - 2 stacked on top of each other next to another 2 molecules stacked on top of each other. I want to analyse the trajectory using a script measuring the distances between the molecules stacked on top of each other, and the molecules next to each other.

If I analyse the trajectory as is I get a lot of jumps in the distance between the molecules stacked on top of each other due to the periodic boundary conditions as one or the other molecule from a pair is going from one end of the box to the other. This is solved by using gmx trjconv -pbc nojump. What I get however is that the two halves of the unit cell end up sliding away from each other, which results in the distance between the side-by-side molecules increasing as the trajectory progresses.

I’ve read the GROMACS documentation, and I’ve seen the comments on researchgate already, and I’ve tried out a bunch of different sequences for trjconv, but I still can’t get what I need which is:

  • having a nojump scenario
  • plus having the molecules all still in the box

Any suggestions as to what I can try?

Thanks in advance.


Maybe this post can help you

Kind regards