Dear all my system contains protein + ligand+ water molecules.
protein + ligand = solute water molecules = solvent I want to do minimization energy in 3 steps : step 1) on protein only step 2) on all solute (protein + ligand) step 3) on all system should I use position restrained minimization energy and use define = -DPOSRES in mdp file? if so, what is my mdp file for each of 3 steps? # step 1: ??? please complete this section. # step 2: define = -DPOSRES_WATER # step 3: I don't use -DPOSRES. In posre.itp file, what is suitable value for force constant? best regards
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