[gmx-users] Umbrella Sampling - Justin tutorial
s.neumann08 at gmail.com
Wed Nov 16 15:58:27 CET 2011
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?
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:
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
On Wed, Nov 16, 2011 at 2:31 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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