Re: ABF with the RMSD colvar

From: Jérôme Hénin (
Date: Fri Jun 07 2013 - 09:07:57 CDT

Hi George,

----- Original Message -----
> Hello
> I would like to set up an ABF simulation to study the conformational
> change
> of a protein using as a colvar the C-alpha RMSD of two conformational
> states.
> What is the reason of defining the
> lowerwallconstant/upperwallconstant
> options;

Typically with a RMSD, you will only need the upperWallConstant, as the natural tendency is to drift away from the

> I am not sure I understand the meaning of the hideJacobian option. Is
> it to be switched on or off?

In doubt, leave it at its default value (no).

> How can I decide on the value of the option fullSamples? By checking
> the
> PMF convergence?

FullSamples affects the early stages of the simulation. Once you're looking at convergence of the PMF, it's a bit late to decide on it. The choice is a trade-off between the speed of the initial exploration, and non-equilibrium work in that period. In doubt, leave it at its default value.

> Is there anything else to check for this particular colvar?

Be aware that you won't see a value or zero, or very small values, and that the PMF will rise steeply for values close to zero. That's just a mathematical property of the RMSD function. To make sure to avoid numerical problems due to this singularity, you could set the lowerBoundary to a small but non-zero number.


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