GROMACS version: 2019.3
GROMACS modification: No
Hi, GROMACS users, i am trying to analyze a lipid bilayer with several phospholipids by extracting several regions, such as a bulk region and interfacial region (water/polar-head interface). I am trying to generate .gro/xtc files only with the molecules implicated in the interfacial region and eliminate those atoms or molecules that don’t belong to the interface. I am using this command to generate a new cubic box for analyzing the regions: gmx trjconv -f new-trj.xtc -s step7_production.gro -box 11.80 11.80 2.5 -trans 0.0 0.0 -1.5 -dump 25000 -o section-low-full.gro. The same command is used for generating the xtc files (without -dump command). I used -trans to move up the new cubic cell to the interfacial region and i made a few analyses such as the gmx msd to compare between the original system, and i observed signficant changes but i’m not sure. The .gro file made by trjconv shows a PBC box in VMD in the interfacial region, but no molecules are removed (Remains the same as the original .gro)
I have the question if i do the analysis of several regions in the bilayer by using the parameters specified in gmx trjconv or if i have to edit my .gro and eliminate those molecules outside the interface.