[gmx-users] Re: umbrella potential

[Justin A. Lemkul]

Stefan Hoorman wrote:

> The distances between the two structures in each of the windows are (in nm):
> 0ps = 1.56 ; 500ps = 1.54; 1000ps = 1.56; 1500 = 1.56; 2000 = 1.52; 2500 
> = 1.65; 3000 = 1.66; 3500 = 1.77; 4000 = 1.63; 4500 = 1.62; 5000 = 1.7; 
> 5250 = 1.62; 5500 = 1.6; 5750 = 1.73; 6000 = 1.85; 6250 = 1.86; 6500 = 
> 1.91; 6750 = 1.84; 7000 = 1.88; 7250 = 1.82; 7500 = 1.93 ; 7750 = 2.04; 
> 8000 = 2.16 ; 8250 = 2.3 ; 8500 = 2.32 ; 8750 = 2.45 ; 9000 = 2.52 ; 
> 9250 = 2.5 ; 9500 = 2.62 ; 9750 = 2.65 ; 10000 = 2.66

There is substantial overlap and jumping back and forth (i.e., 1.56, decrease to 
1.54, increase to 1.56, then back to 1.52, etc) in these distances, so I think 
they are not optimal for umbrella sampling.  Instead of more regular spacing in 
time, I would suggest more regular spacing in terms of distance.  Most 
literature on the topic cites how far apart windows were in terms of distance, 
which is important for WHAM analysis.

-Justin

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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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