[gmx-users] Handling Periodic Boundary Conditions

[Pandya, Akash]

Hi all,

I'm having trouble with visualisation of my system after the MD production run. I have tried the periodic boundary conditions workflow suggested on the gromacs website, although I'm having no luck. I have used the following command to try and obtain a visualisation state that I can work with.

gmx trjconv -f Nonwater.xtc -s non_water.tpr -pbc whole -center -o nonwater.gro

When I visualised this trajectory, my protein molecule appears to have split even though I used -pbc whole. Can someone please help me overcome this issue?

Many thanks,

Akash