MgO nanoparticle deformed in production stage

[ArpitR]

GROMACS version: 2020.1-Ubuntu-2020.1-1
GROMACS modification: No
Here post your question

Hello,

I was working on my MD simulation of a MgO nanoparticle generated from CHARMM-GUI. I was running it in multiple steps of 20ns, and after the first step, when I was checking the results, my nanoparticle started to deform:

(not letting me upload my images because i’m a new member)

I believe that the problem is that while the simulation is running, the water box is deformed to a position in which the nanoparticle starts to exceed the area where it should be, so GROMACs tries to rearrange some of the particles to the other side so that the system doesn’t explode. Or, it might be that CHARMM-GUI set up the file this way for the molecules to rearrange to the other side, and I just need to run this for more time. Any thoughts?

Thanks,
Arpit Ramani

step5_production.mdp (1.1 KB)

[ArpitR]

Here is what it looks like after, it’s supposed to be a cube nanoparticle:

[MagnusL]

That looks fine to me (even if one atom looks a bit misplaced). Molecules crossing the periodic boundary is not a problem, see Terminology - GROMACS 2024.1 documentation and gmx trjconv - GROMACS 2024.1 documentation for more information.

If it helps, VMD can also show multiple periodic images of your system. Check the Periodic tab in Graphical Representations.