[gmx-users] Re: Data Analysis

lloyd riggs lloyd.riggs at gmx.ch
Fri Apr 20 15:12:35 CEST 2012

Dear Justin,

Dont panic.

1) there in cyclic happening at 1/4 the entire run but offset by 2-6 picosecounds between runs.

2) There calculated PMF but the data comes from the origional pullf.xvg files generated if I look at each point (same thing a - or low pullf point.)

-This is precluding the first 2 picosecounds of a 4 ns pulled run as done by another group with similar (90% identical) protein sets (published).

-also in a few after the peak change in energy is reached (around 3.8 ns), I do see fluctuations which I expect due to more free movements.

-I also calculated everything with a single histogram analysis, then did statistics using ploting sofware (qti) for all runs together.  The errors are the same in either case.

-In the end the finalized data (means at any point overall, distances, etc...) are all the same and fit values.  If I exclude the data points I get smooth curves.  If I include them the single point from one of 11 or 1 of 10 runs just seems to effect the error analysis (STD deviation, Standard error) but affects the mean(s) very little.  In the end the mean is all that anyone cares about, along with other associated analysis, but I woundered.

-The errors in half the case ( say around 30 points in all across 22,000 or 20,000 points) are just the mean of the previous and next point but with a negative sign?  In the other half they are always numbers very close to zero (ex: 0.002484890) with the prior or next point around say 30-40.

-The models dont show any wierdness if I print out the pdb for those frames in VMD, so do not know where the error is.  I dont know if its a spring effect, which I assume not if the force is constant, as the pull force is artificial, but I could see it causing a spring effect if the protein(s) one tries to pull apart are strongly bound together (ie say force equivalent in some way to the pull force applied).

Pretty much thats about it.

Stephan Lloyd Watkins

-------- Original-Nachricht --------
> Datum: Fri, 20 Apr 2012 07:35:42 -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: Data Analysis

> lloyd riggs wrote:
> > Dear All,
> > 
> > A question about data analysis.  When Generating raw .xvg files of
> energies I
> > have found say 3-4 points out of 2000 (per run 11 total) is erroneous.
> > 
> > something like
> > 
> >> 20.43534
> > 21.7657 22.212 -34.88 23.680
> > 
> > Something like that.
> > 
> Where are these data from, and how did you conclude that the offending
> point was
> erroneous?
> > Now is there a routine in handling these?  I found when integrating all
> 11 it
> > makes several points error calculations double or triple at a single
> point.
> > Is it proper to remove these when submitting something to generate the
> smooth
> > curve, or are we supposed to include these?
> > 
> You can't just throw away data you don't like without a more rigorous 
> statistical analysis.  You should investigate the source of the weird
> point(s) 
> to see if they might, in fact, be legitimate or generated by an error
> somewhere.
> -Justin
> -- 
> ========================================
> 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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