Re: distanceXY colvar-ABF

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sun Aug 21 2011 - 12:28:07 CDT

Hi Parisa, the ion is not moving "on a circle", it moves in all three
dimensions as usual. The distanceXY just picks those movements that take it
closer to or farther from the axis of reference, and ignores movements
parallel to the axis, or tangent to the "circle". A positive force on
distanceXY will make the ion move away from the axis, negative force will
make it closer.

Giacomo

On Sun, Aug 21, 2011 at 10:05 AM, Parisa Akhski <
Parisa.Akhshi_at_chem.queensu.ca> wrote:

> **
>
> Dear NAMD experts,
>
> In ABF method, I am using "distanceXY" as a colvar to move an ion in XY
> plane and get the PMF profile. I am wondering what negative and positive
> signs of force mean in this case since the ion is moving on a circle
> (defined by the lower and upper boundaries).
>
> Thanks,
>
> Parisa
>

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