[gmx-users] position restrained minimization on the one part of a system

[Atila Petrosian]

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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