[gmx-users] position restrained minimization on the one part of a system
atila.petrosian at gmail.com
Wed Oct 26 14:24:00 CEST 2011
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?
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