GROMACS version: 2024.4
GROMACS modification: Yes/No
Hello,
I made a coarse-grained membrane looking like the composition below:
layer 1: water and ions
layer 2: outer leaflet
layer 3: inner leaflet
layer 4: water and ions
Then after neutralizing, minimizing, and equillibrating, ran my membrane for 10 microseconds with a 25 fs timestep.
When I visualized it in VMD, I realized that layer 4 and half of layer 3 has crossed the periodic boundary and appeared and top so it looked like this:
layer 3: half of the inner leaflet
layer 4: water and ions
layer 1: water and ions
layer 2: outer leaflet
layer 3: the other half of the inner leaflet
I used trjconv -pbc mol and -pbc whole on my membrane but it did not fix it and gave me the same outcome when I visualized it on VMD. I centered my membrane based on my system as well and still did not work. Are there any other ways to fix this?
I am currently running a bigger membrane with more water (thought that maybe there was not enough water to keep them in place.
commands:
gmx trjconv -pbc mol -f production.xtc -s production.tpr -n file_CG.ndx -o production-PBC1.xtc
gmx trjconv -pbc whole -f production.xtc -s production.tpr -n file_CG.ndx -o production-PBC2.xtc
additionally, tried centering too while using pbc mol and whole
Thank you in advance!