Re: ABF 'Xi' log output producing strange results

From: Eric H. Lee (
Date: Thu Aug 27 2009 - 10:48:50 CDT

Actually, zCoord uses the z-axis *projection* distance along your
reaction coordinate, this is a very different concept than just a
restrained straight line along a single axis.

See here:

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC

On Aug 27, 2009, at 10:30 AM, Hugh Martin wrote:

> Hello,
> I wonder if anyone else has experienced this issue: the Xi parameter
> for a zCoord-1atom reaction coordinate (the Cartesian z-axis
> distance between atom abf1 and abf2) is outputting incorrect values
> in my simulations. For instance in one of my simulations, abf1 and
> abf2 are chosen as two oxygen atoms, each belonging to a separate
> water molecule, these are precisely 4.4345 Angstroms apart in the z-
> direction at the start of my simulation, however, in the log file
> the Xi output reads "TCL: ABF> Xi at timestep 0 : 104.585426303",
> this large value of Xi is not the result of a measurement through
> the periodic image, as the waterbox is over 130 Angstroms in height,
> making 104.6 Angstroms impossible in either direction.
> This is a 330k atom system and seems to produce very random values
> for Xi depending on the pair of atoms I choose for abf1 and abf2,
> sometimes being a negative or positive value independent of whether
> abf1 or abf2 is higher in the z-direction. This occurs in both
> NAMD2.6 and NAMD2.71b.
> Any help on the matter will be greatly appreciated.
> Many thanks,
> Hugh

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