[gmx-users] Umbrella Pulling

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 17 16:13:34 CET 2012

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 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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