Re: Colvar orientation of polymer

From: Henrik Schopmans (
Date: Wed Nov 27 2019 - 00:48:13 CST

Hey Giacomo,

thank you for your answer and explanation. I am referring to this answer
(and the one above) in the mailing list:
But it sounds like they were talking about the same thing.

Thanks a lot,

Am Di., 26. Nov. 2019 um 20:16 Uhr schrieb Giacomo Fiorin <>:

> 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).
> Giacomo
> On Tue, Nov 26, 2019 at 1:55 PM Henrik Schopmans <>
> wrote:
>> 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

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:12 CST