GROMACS version: 2023.2
GROMACS modification: No
Here post your question :
I ran a 100ns molecular dynamics simulation of a protein-membrane system where the protein is 10 angstroms away from the membrane. After concatenating the trajectory files and performing post-processing (centering the protein-membrane complex), I noticed that the protein sometimes appears to go below the membrane for some frames in the visualization (Figure 2_462thframe) from the normal orientation (figure1_461thframe).
I’m unsure if this is an issue with the simulation itself or if I’m handling the periodic boundary conditions (PBC) incorrectly during post-processing. I’ve tried various gmx trjconv -pbc options, including -ur rect and -ur compact, but the problem persists.
Could someone please provide guidance on how to resolve this issue in GROMACS?
I think that should work (otherwise try switching the order of step 2 and 3). But keep in mind that this is just a matter of visualisation. If the protein should not be able to pass from one side to the other, e.g., if one leaflet is the “interior” and one is the “exterior”, possibly different in composition, you would need another mirrored bilayer to separate the two solvent volumes.
Thanks very much for the reply. Could you clarify if I should use the -center option along with -pbc mol or just use the -center option on its own for removing periodic boundary conditions?
These are the commands I’m giving for the removing pbc:
1)Command line:
gmx trjconv -s step7_1.tpr -f 100ns.xtc -o test2.xtc -center -pbc mol -n index.ndx
Note that major changes are planned in future for trjconv, to improve usability and utility.
Will write xtc: Compressed trajectory (portable xdr format): xtc
Reading file step7_1.tpr, VERSION 2023.3 (single precision)
Reading file step7_1.tpr, VERSION 2023.3 (single precision)
Select group for centering
Group 0 ( SOLU) has 2047 elements
Group 1 ( MEMB) has 50960 elements
Group 2 ( SOLV) has 100754 elements
Group 3 ( SOLU_MEMB) has 53007 elements
Group 4 ( SYSTEM) has 153761 elements
Select a group: 1
Selected 1: ‘MEMB’
Select group for output
Group 0 ( SOLU) has 2047 elements
Group 1 ( MEMB) has 50960 elements
Group 2 ( SOLV) has 100754 elements
Group 3 ( SOLU_MEMB) has 53007 elements
Group 4 ( SYSTEM) has 153761 elements
Select a group: 4
Selected 4: ‘SYSTEM’
Reading frame 0 time 0.000
Precision of 100ns.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)
Back Off! I just backed up test2.xtc to ./#test2.xtc.1#
Last frame 1000 time 100000.000 → frame 999 time 99900.000
→ frame 1000 time 100000.000
Last written: frame 1000 time 100000.000
Note that major changes are planned in future for trjconv, to improve usability and utility.
Will write xtc: Compressed trajectory (portable xdr format): xtc
Reading file step7_1.tpr, VERSION 2023.3 (single precision)
Reading file step7_1.tpr, VERSION 2023.3 (single precision)
Select group for output
Group 0 ( SOLU) has 2047 elements
Group 1 ( MEMB) has 50960 elements
Group 2 ( SOLV) has 100754 elements
Group 3 ( SOLU_MEMB) has 53007 elements
Group 4 ( SYSTEM) has 153761 elements
Select a group: 3
Selected 3: ‘SOLU_MEMB’
Reading frame 0 time 0.000
Precision of test2.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)
Last frame 1000 time 100000.000 → frame 999 time 99900.000
→ frame 1000 time 100000.000
Last written: frame 1000 time 100000.000
Note that major changes are planned in future for trjconv, to improve usability and utility.
Will write xtc: Compressed trajectory (portable xdr format): xtc
Reading file step7_1.tpr, VERSION 2023.3 (single precision)
Reading file step7_1.tpr, VERSION 2023.3 (single precision)
Select group for output
Group 0 ( SOLU) has 2047 elements
Group 1 ( MEMB) has 50960 elements
Group 2 ( SOLV) has 100754 elements
Group 3 ( SOLU_MEMB) has 53007 elements
Group 4 ( SYSTEM) has 153761 elements
Select a group: 3
Selected 3: ‘SOLU_MEMB’
Reading frame 0 time 0.000
Precision of test2.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)
Back Off! I just backed up trajout.xtc to ./#trajout.xtc.1#
Last frame 1000 time 100000.000 → frame 999 time 99900.000
→ frame 1000 time 100000.000
Last written: frame 1000 time 100000.000
If I follow these steps, I don’t encounter the same problem. However, my membrane is no longer intact (
I don’t think you should need -pbc mol in the first step.
What do you mean that your membrane is no longer intact? Isn’t it just that some residues are drifting outside the periodic box (due to -pbc nojump)? If you visualize the periodic images in VMD (The Periodic tab in Graphical Representations) I think it will look fine. But it might be difficult for you to prevent the protein from jumping and still having the lipids to jump.
Thank you for your feedback. I have checked the visualization using the Periodic tab in VMD to verify that it appears as intended. However, I still need to understand why the lipid residues are shifting and why the protein sometimes moves outside the PBC box. Could you provide some insight into managing trajectories in these situations, especially since PBC removal can be confusing for beginners? I am finding it challenging to keep the protein within the box while allowing the lipids to move. Do you have any suggestions on handling this effectively within the constraints of periodic boundary conditions?
It is not strange that the lipids are shifting and that the protein moves. Remember that the system is periodic (repeated infinitely) - atoms crossing the edge on one side enter on the other and all interactions are calculated across the periodic boundaries.
The treatments you have done using gmx trjconv help visualizing the system in a way you are more used to, but there is no difference in the atom locations. Making a molecule whole across periodic boundaries may definitely help the understanding. Preventing molecules from jumping can also make it easier to view a trajectory, but, as you notice, it also makes the molecules drift away from each other (in a visual representation without showing the periodic images) making it seem like there are gaps in the molecular system. I think you will learn a lot by using the periodic representation in VMD of the original trajectory and after each of the gmx trjconv steps you have done. I think you will understand better how it works. You can also experiment with the -ur compact option, but I think that helps more for systems with non-triclinic box types.
For analysis purposes, it does not make a difference what pbc treatments you have applied, but I usually recommend using the original trajectory.
