[gmx-users] Re: Re: Re: Re: Re: Re: Re: Re: umbrella potentia

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 25 12:40:50 CEST 2009

Stefan Hoorman wrote:

> I simulate 400 ps for each window. I have a total of 20 windows. My 

400 ps is relatively short, especially given the speed of current hardware and 
of Gromacs 4.0.  I generally see longer time periods in the literature.

> histogram looks like a chromatographic peak ranging from 0.74 and 0.91

Then you are not getting the separation you described before (>2.5 nm).  It 
looks like you are only pulling a distance of 0.17 nm total.

> in the x axis and the count (y axis) goes up to 30000. Is there a way to 
> index my histogram.xvg or my profile.xvg file and send it to the gromacs 
> user's list? Or is it not necessary?

The best way to send this information is to generate image files and post them 
to a free site where others can see them (photobucket, etc).  Up to you to 
determine whether its necessary.  At this point, I think you are just not 
getting what you think you are setting up.


> Thank you
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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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