Re: Issues with 'Gyration' in Colvars module

From: Aron Broom (
Date: Wed May 23 2012 - 14:56:49 CDT

Hi Shaon,

I've no idea about 1), but for 2), what happens if you specifiy Rg to be
within 4-7 rather than 5-7? From my understanding the ABF method needs to
sample forces before it starts to apply a bias, so if you're system starts
outside the biasing range, it will never collect any samples, and hence
never start to apply a bias. That would be my first thought anyway. If
you really want to do 5-7 angstroms, you should apply a harmonic potential
on Rg and sit it ~6 angstroms in order to equilibrate the system before
running ABF.


On Wed, May 23, 2012 at 3:48 PM, Shaon Chakrabarti <> wrote:

> Hi NAMD experts,
> I'm facing two problems with the gyration component in
> the Colvars module.
> 1) The NAMD user's guide says that the radius of gyration
> is defined using the Center of Geometry. However, when
> I write my own code (using the COG definition) to compute
> the Rg of a molecule, the Rg value is always about 0.2
> angstroms more compared to the output in the 'colvars.traj'
> file. The values from my code exactly match the values
> I get if I use the 'measure rgyr' command in VMD. I also
> computed Rg using Center of Mass, but that makes the
> difference even larger. I'd be grateful if someone can tell
> me if I'm making a mistake somewhere, or if Rg is
> actually defined differently in the Colvars module.
> P.S. My molecule (about 30 angstroms long when fully
> extended) is in the middle of a water box of side 55
> angstroms.
> 2) The second problem is similar (as I understand from
> the threads in 2008) to what Subramanian
> Vaitheeswaran faced while using the gyration
> component with ABF. If I specify the Rg to be (say)
> within say 5 and 7 angstroms, and use ABF to get
> the PMF, the system hovers at Rg value around
> 4.5-4.8 most of the time! A final resolution doesn't
> seem to have been posted back in 2008, and it
> would be of immense help if someone could tell
> me what's going on....if the problem has been
> resolved. I tried switching the hideJacobian option
> to yes, and increasing the lower and upper wall
> constants, but these don't make any difference.
> It would be great if someone could help with these two issues.
> Thanks,
> Shaon

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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