Hi everybody, I want to minimize only the hydrogen atoms of my protein but NOT the rest of it. For this reason I use a restriction file produced by pdb2gmx with the -i option. But still the atoms are minimized a bit. Because when I calculate the RMSD with the program g_confrms of my structure before and after the minimization ignoring the hydrogen atoms (Protein-H) the RMSD value is 0.115466nm. SO is there are possibility to completely fix those atoms. So that they just do not move?
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