[gmx-users] Re:WHAM question

lloyd riggs lloyd.riggs at gmx.ch
Thu Apr 19 11:04:24 CEST 2012

-------- Original-Nachricht --------
> Datum: Wed, 18 Apr 2012 10:49:00 -0400
> Von: "Justin A. Lemkul" <jalemkul at vt.edu>
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Betreff: Re: [gmx-users] Re:WHAM question

> 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

Dear Justin,

I tried it once, yes g_dist contradicts it well and gives the actual distances dy between the COMs.  Also, If I (I did this weeks back) use I think g_analyze or the utility which gives coordinates, print out the Y coordinates for the COM of the pulled group and it is the secound column printed to the pullx.xvg file.  The Gromacs instillation has been taken ove by the Chem/Computer admin so they are now responsible for it.  I also have it on my home PC, but can only use auxillary analysis scripts as it would take 1 year to run something unless I ported things to openCL, which would probably take me personally XX years.  I think however I am the only one using Gromacs here except for a 1 or 2 times a year course from the chem department....as the problem is only with the instillation here I dont know if it is a bug, or maybe an instillation problem, or something else (seems like only a 2 line get and print to file thing could do that though, or it skips the A-B=delta portion of
  the script which I have no clue where is located?)


Stephan Watkins

> -- 
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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