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?
Hello Smith, I recommend centralizing only the membrane. You can create an index to combine the lipids if you're using different types. Additionally, there isn't any problem with your simulation box or the PBC. When the simulation starts, it's normal for the protein to move as it interacts freely with water and ions. I also recommend letting the simulation continue. When your protein begins to interact with the membrane, if that's the case, it will have less movement.
Best regards.
Hello Smit, You can use -pbc nojump with gmx trjconv on your trajectory file (.xtc/.trr) to remove the jumps and then use -pbc mol -ur compact to keep the system together. This may help.
Zuriel González Carrera Indrani Bera Thank you for the feedback and apologies for the late response, I've encountered an issue where the lipid bilayer at the edges of my simulation box appears to disintegrate over time, despite centering the trajectory on the membrane and applying 'pbc whole' and 'pbc no jump'. This is causing the membrane to lose its original shape. I'm not sure what's causing this or what post-processing steps I should take to maintain membrane integrity.
Is this behavior normal, or should I be concerned about proceeding with further analysis? If so, what specific post-processing steps or adjustments to my workflow would you recommend to ensure the membrane remains intact throughout the simulation?
steps i followed:
gmx trjconv -center (on membrane)
gmx trjconv -pbc whole (on protein+memb)
gmx trjconv -pbc no jump (on protein+memb)
Hello Smit Patel,
I apologize for the late response.
What force field are you using? That can also affect the behavior of the lipids.
Anyways, I believe there is no issue with your system. I would recommend building a membrane control using the same conditions and lipid types, and performing APL, thickness, and density analyses for comparison.
Additionally, the way you visualize your system can change by using either "Perspective" or "Orthographic" visualization modes. Check the attached images for the differences.
Best regards.
To fix the PBC problem for a protein-membrane system in GROMACS:
All of which can be easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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