[gmx-users] Umbrella Sampling - Justin tutorial

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 16 15:31:56 CET 2011

Steven Neumann wrote:
> Hi GMX Users,
> I am doing Justin tutorial of Umbrella sampling. I have just finished 
> continous pulling of chainA from the reference chainB. I have some 
> questions. I looked at the trajectory of pulling and it has began with 
> dissociating residue 27Alanine from the ChainB following 26, 25, 24...1. 
> My question is why? As you apply pulling with the constant force to the 
> COM of the whole chain why does it start with terminal residue following 
> then one by one? Why not the middle one or any other?

By pulling on the COM of any molecule, the forces are then redistributed to the 
other atoms.  In the case given in the tutorial, the region you see dissociate 
first is held together by relatively weak interactions.  If you pull directly on 
a specific residue or atom, that residue will dissociate first in all 
likelihood.  For further discussion pertinent to this specific system, please 
refer to our paper linked from the tutorial.  You're observing what we observed, 
so there is no problem and I am happy that the behavior is reproducible for 
others :)

> The second thing I would like to extract starting configurations from 
> from my pulling. Till frame 189 the COM varies from 0.49 to 0.56 - makes 
> sense as the ChainA is still within ChainB. I would like to use 
> configurations:
> 0 - 0.50
> 50 - 0.52
> 100 - 0.51
> 150 - 0.51
> 200 - 0.62
> 250 - 2.21
> ....
> 500 - 5.48
> My question is: Do I have to use exactly the same e.g. 0.2 nm spacing or 
> this configuration above is ok? Can the spacing in nm vary?

I'm not clear on what you mean here.  In constructing a reaction coordinate, you 
need to sample at finite intervals along the given path.  0.2 nm is a common 
spacing used for many systems, and if you want to reproduce the tutorial's 
results, you should use that spacing.  Otherwise, I can't guarantee what you 
will see.  The peptide chains remain bound for a long time, until the force 
applied by the harmonic spring overcomes the intermolecular interactions.  This 
was useful in our study (again, see the paper for why).

> And the last thing - is it required to use frames till 189 as the COM 
> varies in this area?

You only need one to represent the center of that particular window, since the 
COM distance isn't changing much here.



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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