Re: Zcoord for ABF

From: Jérôme Hénin (
Date: Wed Dec 22 2010 - 15:11:29 CST


On 17 December 2010 20:22, Parisa Akhski <> wrote:
> Hi,
> In  ABF (NAMD 2.6), I see that the difference between "zCoord" and
> "zCoord-atom" is that the first one stands for the selection of a single
> atom of interest while the second one is for a group of atoms of interest. I
> am having a single ion , moving along the channel so, I have to use
> "zCoord-1atom". However, I realized that I made a mistake in preparing my
> configuration file (I used "zCoord" and addressed just one ion for atom
> selection" and I didn't get any related error during the simulation. Now the
> simulation is finished. Are the results reliable or I need to repeat that
> with the right command (zCoord-atom)?

Your results are all right.

> I have another question:
> My understanding from zCoord or zCoord-1atom is that we rotate the system to
> put the channel along Z axis first and The program always takes this as the
> Z axis during the simulation. Then we define two groups as "the reference
> atoms" and "the ion of interest", and we also define two boundaries (let's
> say 7 and 10). Then the program is supposed to move the "ion of interest"
> along channel "z axis" from "7 A" to "10 A" with respect to the COM of the
> "reference atoms". Right?


> However, in my system and I think in all the
> systems both the "reference atoms" and "the ion of interest" are moving
> freely so that the distance I defined at the beginning "7 to 10" is not
> staying the same anymore unless we fix the atoms to stay there or the atoms
> move really slow. I am wondering If we we don't fix the atoms and let them
> move freely , how does the program work to move the ion between "7 and 10"?
> I mean does the program always refer to the very first definition of atom
> positions and apply the "distance 7 to 10" to this? or somehow, it
> compensates for this movements so that the area of sampling is still between
> 7 to 10 as we defined. Or does the program calculate the COM of the
> reference for each time step and moves the ion with respect to that between
> "7 and 10"? This way in the case of fast movement if there is no fixed
> atoms,... there is no guarantee that the sampling area is the same as what
> we expected. Right?

Sorry, you lost me there. What matters is relative motion of the ion
and the reference group. Everything moving around is not a problem.

> I apologize if my questions seem naive. I ran my simulation without fixing
> any atoms and I figured out that in all simulations the whole system is
> moving which causes the ion not to be along Z axis in some windows anymore.

The coordinate is a projection. It does not know or care if the ion is
'along the z axis'. That depends on the x and y coordinates - it is
your job to care about those. If they need to be restrained, you can
do that.


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