Re: A problem in ABF simulation

From: Karteek Bejagam (
Date: Tue Nov 29 2016 - 12:14:44 CST


Why do you want RMSD to constrain within in a narrow channel ( just 0.2 A).

Value of 3.1 is not surprising since the boundaries are not hard ones.
Did you perform unbiased simulation (regular ones) before running ABF
simulations to see the RMSD values?
If the values are way off, do you want to reconsider the regions?

How are the RMSD fluctuations for the unbiased simulations? Are they less
than 0.2 A (your specified region)?
If not, I would strongly suggest you in increasing the region.

Hope this helps.


On Tue, Nov 29, 2016 at 9:16 AM, Jérôme Hénin <> wrote:

> Hi,
> You probably don't want to use the hideJacobian option for a RMSD. The
> Jacobian term is very large for that coordinate (see the paper for the
> equations
> )

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