Visualizing clusters of molecules with trjconv with pbc

GROMACS version: 2016
GROMACS modification: No

I am running simulations which involve some proteins and some lipids which end up forming a cluster. I am having some issues visualizing it in some cases where the cluster of the molecules crosses the periodic boundary conditions. An example is below:


Proteins are blue and lipids are grey (with other colors highlighting residues or atoms in the lipids to determine termini and lipid orientation). The two large clusters of grey appear to be part of one larger cluster broken across the boundary conditions. I am having trouble figuring out the correct way to “stitch” this together using gmx trjconv. I have tried the following:

  • each type of pbc option. The cluster option actually broke this system up into multiple small clusters, > 4, which clearly is not the case here (at least from my perspective). whole and mol inherently do not help here except keeping molecules whole.
  • I have incorporated “-ur compact”
  • Using “-center yes” for any group (Protein, Lipid, Protein + Lipid using an index file, the whole system) does not help and only shifts the box at best.

There are total of 98 residues so I’d like to avoid the manual labor of finding which lipids are across the box and just doing to calculation by hand to change the coordinates. I am using VMD to visualize in case that’s useful. Would anyone have some suggestions for how to tackle this problem?

Thanks in advance!