# [gmx-users] Umbrella Sampling - Justin tutorial

Steven Neumann 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:

189 0.5769072

190 0.5753590

191 0.5711223

192 0.5719844

193 0.5856807

194 0.5886649

195 0.5958101

.......

211 0.7111782

212 0.7322708

213 0.7675126

...

378 4.2101626

379 4.1993918

380 4.2223649

......

500 5.48839

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
5nm?

Thank you,

Steven

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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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