Colvar orientation of polymer

From: Henrik Schopmans (
Date: Tue Nov 26 2019 - 12:53:21 CST

Dear NAMD users,

I'm simulating a large polymer (20+ monomers) in water and want to use a
harmonic colvar bias on the orientation to be able to use an anisotropic
simulation box.
I have two general questions concerning this approach:

- For better performance, I don't want to use all atoms of my polymer for
the colvar, but say just one carbon atom per monomer.
I found in the mailing list that this is safe to do and no internal degrees
of freedom are affected. But how can this be?
The forces are only applied to the atoms I specify, right? If I include all
atoms of my polymer in the colvar, I can understand why
the internal degrees of freedom aren't affected. But what about the extreme
case where I for example only select the two end-atoms
of my polymer? How does this work?
- I am applying forces to my polymer to fix its orientation, but I don't
apply these forces to the water molecules (of course).
How can I be sure that these forces don't affect the overall dynamics of my
system (polymer + water)?

Thank you very much in advance and have a nice evening,
Henrik Schopmans

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