From: Scott Boyken (sboyken_at_iastate.edu)
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
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:
#restrain.pdb Beta column set to 1 for protein
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 sboyken_at_iastate.edu (515)-294-0781 Biochemistry, Biophysics, and Molecular Biology 4288, Molecular Biology Building Iowa State University Ames, IA 50011
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