Re: ABF 'Xi' log output producing strange results

From: Jerome Henin (
Date: Thu Aug 27 2009 - 16:39:35 CDT

Just making sure of one thing - you are providing ABF with 1-based
atom indices, as in PDB files, not the 0-based indices from VMD? In
VMD, the 1-based index is called "serial".

Eric: thanks for replying. I think Hugh is using zCoord from the NAMD
2.6 implementation, not the more flexible distanceZ from the colvars


On Thu, Aug 27, 2009 at 11:30 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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