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
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists