[gmx-users] Re:WHAM question

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 18 16:49:00 CEST 2012

lloyd riggs wrote:
>> When accusing the code of doing something wrong, "I don't know" isn't a
>> >very good justification ;)  The contents of pullx.xvg are the COM
>> >Acoordinates of the reference group on the axis or axes along which the
>> >restraint was applied, followed by the distance between the reference and
>> >pulled group, again along each axis.  In your case you should have the
>> y->coordinate of the COM of the reference, and dY, which represents the
>> >distance between the two groups along the y-axis only.  These values
>> >should be easy to confirm with g_traj and g_dist.
> My pullx.xvg file, as I think I mentioned, prints the refernce coordinates
> and the coordinates of the COM of the pulled group.  I can in a spread sheet
> (minus the reformating 10 times) just make a column of the dY.
> My question, do you or anyone know why it prints the reference and pulled COM
> rather than the pulled COM and dY?  Can somone compile something that way, or
> is it some bug or maybe just something to do with the N Y N vs. N N Y
> pulling?

The content of pullx.xvg (according to the headers and the explanations I have 
seen) is indeed the COM of the reference and dY, not the coordinate(s) of the 
pulled group.  Does g_dist contradict these assertions?  I am basing my 
knowledge on its contents based on the printed header and statements from the 
developers, but if something has gone wrong here, it's an important (potential) 
bug to fix.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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