[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
> 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
> 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users