[gmx-users] Umbrella Pulling

[Justin A. Lemkul]

Steven Neumann wrote:
> 
> 
> On Fri, Feb 17, 2012 at 2:52 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Steven Neumann wrote:
> 
> 
> 
>         On Fri, Feb 17, 2012 at 2:12 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
> 
> 
> 
>            Steven Neumann wrote:
> 
>                Hello Justin,
> 
>                As you recommended I run longer pulling of my ligand. I
>         pull the
>                ligand which is on the top of my protein so the top of the
>                protein is pulled so that the whole protein rotated app. 30
>                degrees - the low part of the protein came out of the box
>         due to
>                the rotation. After app 600 ps the ligand does not move
>         any more
>                and the force applied increase linearly. As I saw the
>                trajectory, ligand does not collide with a periodic image
>         but it
>                does not move. Please, see attacheg plot force vs time.
>         Can you
>                explain why the force increase linearly and ligand is not
>         pulled
>                any more? This is my mdp file for pulling:
> 
> 
>            Is the pulled distance greater than half of the box vector in z?
>             That's the only reason I can see things going haywire.  With
>         simple
>            "distance" geometry, there are some limitations like that.
>          Rotation
>            itself is not a problem.  You're separating two objects;
>         there's no
>            clear orientation dependence in that case.
> 
>            -Justin
> 
> 
> 
>         As you can see the pulling distance is 5 nm. The lenght of my
>         box in Z direction is 12 nm. Thus, it is not. Any other ideas?
> 
> 
>     No, it's not.  You're doing 1 ns of simulation (contrary to the
>     comment, 500000 * 0.002 = 1000 ps) and thus pulling at 10 nm per ns
>     you are trying to pull 10 nm in this simulation.  So once your
>     molecule hits 6 nm (right at about 600 ps from your plot and the
>     expected pull rate), you're violating the criterion that I suspected.
> 
>     -Justin
> 
> 
> Yep, you are right. I made a mistake with my mdp files. Is there any 
> particular distance the ligand should be pulled away from a protein as 
> its interaction is via hydrogen bonds and hydropobic forces only?
> 

Ideally, you pull to achieve a sufficient distance that the species are no 
longer interacting.  With PME, that's impossible, so the goal should be 
sufficient distance that the interactions are negligible.

-Justin

-- 
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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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