[gmx-users] Umbrella Sampling tutorial

[Justin A. Lemkul]

Steven Neumann wrote:
> Hey Gmx Users,
>  
> I went through Justin tutorial of umbrella sampling with spacing of 0.2 nm:
> Time  COM distance
>    0  -  0.5
> 208 -  0.7
> 218 -  0.92
> 225 - 1.119
> 231 - 1.41
> 235 - 1.61
> 239 - 1.81
> 246 - 2.09
> 253 - 2.3
> 261 - 2.51
> 268 - 2.71
> 276 - 2.91
> 289 - 3.11
> 307 - 3.3
> 325 - 3.5
> 348 - 3.7
> 359 - 3.93
> 371 - 4.1
> 388 - 4.3
> 412 - 4.51
> 423 - 4.7
> 450 - 4.92
> 454 - 5
>  
> Together 22 windows. I obtained delatG= -37 kcal/mol
>  
> Do you have any clue why is that so far away from the value from 
> tutorial of -50.5 kcal./mol?
>  

Not really.  You don't have the even 0.2-nm spacing that the tutorial calls for, 
but I know others have reproduced the value, so it should certainly be possible.

-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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