[gmx-users] Re:WHAM question

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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