Fixing atoms during simulation

From: Uma Mahankali (
Date: Sat May 07 2005 - 19:33:49 CDT


I read through the posts regarding the fixingatoms option but it still
doesn't work for me.
I have a pdb file with the fifth column X for just the protein part
and this is what I have in my configuration file:

fixedAtoms on
fixedAtomsFile src/solv3_box_namd_fixed.pdb
fixedAtomsCol X

However, when I do this and run a short minimization, ALL of the
structure is fixed. I have all the coordinates from the original pdb
file in the fixed pdb with just the added 'X' in the fifth column for
the atoms to be fixed.

I just moved from Charmm to NAMD and I am lost..

Could someone help me out please?

Uma Mahankali

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