Re: Colvar orientation of polymer

From: Giacomo Fiorin (
Date: Tue Nov 26 2019 - 13:16:04 CST

Hello Henrik, for the first question it would help if you mentioned what
was said in the mailing list message you refer to.

In general, biasing forces applied on collective variables will vary much
more slowly than the forces from the interatomic interactions. You can
verify this yourself by checking the atomic forces for the same snapshot
with and without a Colvars restraint. You may find forceDCDFile useful:
or the loadforces command:

Because the external forces are smaller and vary more slowly than the
interatomic forces, you can assume that the effects of the former are
propagated to all the atoms via the latter.

For the effects on water, I'm not sure what potential issues are you
thinking about: even though you are using a very elongated unit cell to
save water molecules, you should always include enough water to have fully
decorrelated water at the edges (restraint or no restraint).

One thing that comes to mind is the contribution to the pressure tensor
coming from the external forces. Although this is included in the
dynamics, an orientation restraint specifically also happens to have
negligible contribution (a rotation won't try to stretch or squeeze the
unit cell).


On Tue, Nov 26, 2019 at 1:55 PM Henrik Schopmans <>

> 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

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD

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