Constrain atoms in NAMD.

Previously, I used fixed atoms in NAMD. But I cannot make the simulation run. Errors!!!

I found that constraining atoms could solve the problem. You may find information how to constrain atoms. But I am confused about how to set constrain force. And I found solution at http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2009-2010/0751.html.

constraints on
consref restraint.pdb
conskfile restraint.pdb
conskcol B
constraintScaling 3.0

if you wanted to set the force constant to 3 kcal/mol/A^2

 

Why people don’t explain the detail in the manual?

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