GROMACS version: gromacs/2023.2
GROMACS modification: No
Hello everyone,
I’m currently working on a membrane protein that forms a dimer, comprising two monomers with residues numbered from 1 to 655. This results in a total of 1310 residues. I’ve noticed differences in the RMSD plots when using a .gro file versus a .tpr file as the reference input in the following command:
gmx rms -f equilibrations.xtc -s equilibration.tpr -o rmsd.xvg
When calculating RMSD using the .gro file, I’ve observed spikes in the 5th and 6th equilibration runs. I conducted a total of 6 equilibration runs, each with varying durations (125.125, 125, 500, 500, 500 ps) and decreasing positional restraints. You can find the plots I generated here.
Please note that I created the input files using CHARMM-GUI, and the minimization step altered the numbering of my dimer protein. Specifically, the .gro file (minimization.gro) contains two monomers with residues from 1 to 655, whereas the one from CHARMM-GUI has the dimer spanning residues 1 to 1310. This is the only difference I’ve identified in the .gro files.
Thank you for your assistance and insights.