[gmx-users] Umberella sampling

[Justin A. Lemkul]

mohsen ramezanpour wrote:
> Dear Dr.Justin
>  
> I had asked this question before but unfortunately I didn't answered good!
> 
> Instead of Pulling and separating some structures in definite distances,
> I located my drug in definite distances along z axis (as my initial 
> structures for doing umbrella sampling).
> Am I right?
> 

I have no idea.  Presumably, if you've defined the reaction coordinate 
appropriately and distributed configurations along this vector at adequate 
intervals to sample the whole coordinate, then yes.

> The main problem underlying this question is :
>  
> Do we need to know the velocity of drug in every structure we choose for 
> doing umbrella sampling?(do they need to include the velocities too?)

PMF is calculated from either the resulting positions (in pullx.xvg) or forces 
(pullf.xvg) from the harmonically restrained simulations.

> if no,which criteria assures with this K our molecule can cover the 
> length of it's windows?
> 

You can't necessarily know a priori if your force constants are adequate. 
Unfortunately, it's a bit empirical.  Run some simulations and analyze the 
result with g_wham.  A smooth PMF with good overlap between the histograms 
indicates your sampling is (at least) good, if not optimal on the first try.

> Because I have chosen windows with different lingthes,And I want now to 
> choose K so that it can sweep the lengthes.
> 

Weaker force constants allow for more oscillation, but again, there is no 
prescribed way to know what values to choose.  If you have some very large 
window, you assign a weaker force constant, but then you may not cover the 
entire sampling window without a longer simulation in this window such that your 
molecule wanders through all of the applicable configuration space.

-Justin

> Thanks in advance for your reply
> 
> 
> 
> 

-- 
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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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