Re: Issues with 'Gyration' in Colvars module

From: Shaon Chakrabarti (
Date: Sat Jun 02 2012 - 14:29:52 CDT

Hi Giacomo,Aron and Jerome (Jerome--thanks a lot for sending me the source
   Really sorry for taking so much time to get back to you'll--we were
perilously short of computer time in our group, and I was waiting for the
month to end to get some new computer time. Sorry if this causes

Jerome--I had included hydrogen atoms in my calculation of Rg and so the
results I mentioned in my previous email had hydrogen included.

Answer to Aron's question--yes, every time I start a simulation from a pdb
and psf generated from the middle of a dcd file, I recalculate the center
and minmax of that frame using VMD. Because of NPT simulations, the
box size does vary a bit, and I've been careful about that aspect.

About your suggestion,Aron---it seemed very reasonable to me, and I tried
it out...but the result is still the same! The system stays stuck at Rg
7.0 all the time! I am attaching my colvars config file and the
file showing a 0.2 ns run, including applied forces.


On Fri, May 25, 2012 at 11:20 AM, Jérôme Hénin <>wrote:

> [re-sending in clipped form to avoid mailer issues]
> Hi Shaon,
> As Giacomo noted, there is a discrepancy between what's implemented
> and what is documented - this probably escaped us because our typical
> test cases have atoms with identical masses. That may well be the
> cause of your problem, because the Jacobian used for the ABF
> implementation is definitely that of the unweighted function. For this
> kind of variable, the Jacobian correction always yields a biasing
> force that pushes toward small values, and increases as 1/Rg.
> Did you include hydrogen atoms in your definition of Rg? That would
> make it more sensitive to this issue.
> In any case, the code calculating this should be changed. We have a
> fix in the works: the mass weighting will become optional to
> accommodate all cases. In the meantime, I am attaching a source file
> that disables it, if that's any help.
> Best,
> Jerome

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:03 CST