[gmx-users] Umbrella Sampling - Justin tutorial

[Justin A. Lemkul]

Steven Neumann wrote:
> Thank you Justin, now I get what you mean!
> As I understood I should pick just one frame untill 189 ps (when 
> dissociation occured) - does it matter which one I will choose on the 
> final binding free energy?

The free energy minimum should (theoretically) be when the peptides are still 
interacting, i.e. at time zero.  Use this frame and base the spacing off of it.

> Then spacing should be 0.2 nm. Right? But how is it possible to do 
> spacing like this from such results of summary_distances.dat:
>  
> 
> 189 0.5769072
> 
> 190 0.5753590
> 
> 191 0.5711223
> 
> 192 0.5719844
> 
> 193 0.5856807
> 
> 194 0.5886649
> 
> 195 0.5958101
> 
> .......
> 
> 211 0.7111782
> 
> 212 0.7322708
> 
> 213 0.7675126
> 
> ...
> 
> 378 4.2101626
> 
> 379 4.1993918
> 
> 380 4.2223649
> 
> ......
> 
> 500 5.48839
> 
> Do you mean the approximate valueof 0.2 nm spacing? As it would be 
> difficult with these numbers. Can you e.g. do spacing of app. 0.1 nm 
> until e.g. 3 nm and then increase it to 0.2 nm (I think as in your 
> paper) until 5nm?
> 

Choose approximate values.

My protocol of uneven spacing was necessary to refine the energy minimum for the 
suitable data for the paper.  I kept the tutorial simple; you should still 
achieve a reasonable result.  Uneven spacing is uncommon in the literature, so I 
did not want to give anyone the impression that it was a standard protocol, 
leaving it as an exercise for the reader to understand the paper and the 
motivation for uneven spacing.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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