PBCs in a slightly complex system

User discussions
1

Hi everyone,

I have a system made up of:

  1. Two protein chains (not interacting, that was the purpose of the simulation to see if they do).
  2. ~ 100 molecules of hexanediol.
  3. water and ions.

after the simulatioin is complete, I was trying to remove the artifacts caused by the PBCs. I tried different tricks and combinations, but nothing worked as intended (we need everything to be in its original shape/form, no diffusion, no any sort of PBCs). There is always a problem left with something. Here is what I did

; I extracted a sample to try things on

gmx trjconv -s production_run.tpr -f production_run.xtc -o sample.xtc -skip 10
0 (system)

First, I tried
gmx trjconv -s production_run.tpr -f sample.xtc -o mol.xtc -pbc mol -ur compact -center -trans 10 10 10
0
(protein chains still jumping)
gmx trjconv -s production_run.tpr -f sample.xtc -o mol.xtc -pbc res -ur compact -center -trans 10 10 10
0
(protein chains still stretching)

; Then I tried a different approach based on the suggested workflow (here), I made it whole

gmx trjconv -s production_run.tpr -f sample.xtc -o made_whole.xtc -pbc whole
0

up to this stage, water molecules, hexanediol, and protein are fine without stretching or any funny appearance. The only thing is that the protein chains are still jumping. Here is what I tried

; extracted the first frame
gmx trjconv -s production_run.tpr -f sample.xtc -o first_frame.pdb -dump 0
0

; I invoked the nojump option:

gmx trjconv -s first_frame.pdb -f made_whole.xtc -o whole_no_jump.xtc -pbc nojump
0

It destroys the box (it’s now a sphere instead of the 10x10x10 cube), the proteins, the hexanediol molecules, and the water molecules. Everything, except ions now has artefacts.

I tried to wrap it back to a box
gmx trjconv -s production_run.tpr -f whole_no_jump.xtc -o whole_no_jump_centered.xtc -center -n index.ndx
X (I tried centered on the system, the hexanediol, the protein, a single chain even though they are not interacting), nothing worked!

The option -pbc mol -ur compact introduces the jumping again. Even the other option for -pbc (res).

I even tried

Any recommendation is highly appreciated.

Kind regards,
Jameel

2

You cannot both have everything in the box and not jumping.

If you are lucky, you might be able to get a non-jumping pair of proteins. But that is not guaranteed, as it will depend on how the proteins move. For that you need to first run -pbc nojump, without the whole step before (assuming molecules are whole in your tpr file). Then center the result on the COM of the two proteins. And then run a third step with -pbc mol -ur compact.

3

Thank you @hess so much for your reply!

I tried that before and now after receiving your reply. To double check that the molecules are not broken in the production_run.tpr file, I invoked

gmx editconf -f production_run.tpr -o prod.gro

and visualized the structure in PyMOL, nothing is broken at all.

I executed the commands you recommend in the correct order, but I still get PBC artifacts on water molecules from all sides of the box that gradually become severe as the trajectory continue. I tried the -pbc mol -ur compact with and without -trans 10 10 10 but the outcome is the same as in the image below.

Nik
Nik1872×576 183 KB

Thanks again and kind regards,

Jameel