constraintScaling to gradually release harmonic restraints during minimization

From: Scott Boyken (
Date: Tue Jul 20 2010 - 15:22:08 CDT


I'm trying to run several rounds of minimization and equilibration on a
protein in preparation for a simulation, but I need help on deciding values
for constraintScaling. Here's what we're hoping to do:

1. Run minimization and equilibration on protein solvated in water box with
protein constrained (using fixedAtoms)
2. Run minimization using harmonic constraints on the protein, which are
gradually released
3. Run minimization and equilibration in which entire system (protein and
water) is allowed to move

For step 2, it would look something like this:

constraints on
consRef restrain.pdb
consKFile restrain.pdb
#restrain.pdb Beta column set to 1 for protein
consKCol B

constraintScaling 100
minimize 1000

constraintScaling 50
minimize 1000

constraintScaling 25
minimize 1000

constraintScaling 0
minimize 1000

Can anyone recommend reasonable values for constraintScaling? (i.e. is 100
too strong? should we reduce in smaller increments?).

Is this approach reasonable? Or is there a better way to minimizing and
equilibrating to set up a system?

Any suggestions would be greatly appreciated. Thanks!
Scott Boyken

Scott Boyken
Biochemistry, Biophysics, and Molecular Biology
4288, Molecular Biology Building
Iowa State University
Ames, IA 50011

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