Hello, I`m trying to run
MD for a extracellular domain of a receptor-protein complex, but the rmsd is not stable. I used charmm36 2022. can you tell me if the RMSD is normal? I want to compare it with another complex that its extracellular domain is the same, but the protein ligand is different. is the RMSD good enough to be compared? after md, I used these cods: 1- gmx trjconv -s md.tpr -f md.xtc -o md_nojump.xtc -pbc nojump system
2-gmx trjconv -s md.tpr -f md_nojump.xtc -o md_centered.xtc -pbc mol -ur compact -center protein system
3- gmx trjconv -s md.tpr -f md_centered.xtc -o md_fit.xtc -fit rot+trans backbone protein
4-gmx rms -s md.tpr -f md_fit.xtc -o rmsd.xvg -tu ns backbone backbone I found another article about MD of this complex, it used minim in vacum with emtol 10, I can`t get to the emtol less than 350. please help me.