Steven Neumann wrote:
On Fri, Feb 17, 2012 at 2:52 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Steven Neumann wrote:
On Fri, Feb 17, 2012 at 2:12 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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
--
========================================
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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