[gmx-users] Re: Data Analysis

lloyd riggs lloyd.riggs at gmx.ch
Fri Apr 20 16:18:19 CEST 2012

> This sounds to me like a periodicity issue.  Were these runs conducted
> with 
> "pull_geometry = distance"?  If so, were the COM distances always less
> than half 
> of the box vector along the restrained dimension(s)?  Are you running with
> NPT? 
>   If the answer to any or all of these is "yes," then you could have a
> problem 
> with the pull algorithm failing due to periodicity.  The sign changes
> might 
> account for that.  You wouldn't see any weird periodic jumps, but the size
> of 
> the box and the COM distance at the instance of the sign/magnitude change
> would 
> coincide.


As the swiss say.  At the very end one or two amino acids look out of the box into the botomn again in 1 run especially.

>A mean is only as good as the error associated with it.  No error >estimate, no confidence in the value.

Well I trust the results except one or two points.  The means stay the same between the mentioned points, but the STDDEV and STD error double, as it is 2000 points or so, it just looks like a smooth curve with a linear (really leanear) spike.  I dont thinks its that big an issue though comparativly, as one does not loose the overall curve reguardless.

Thanks for your advice, suggestions and knowledge base.


Stephan Watkins

> -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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