[gmx-users] Re: "Impulsive" motion resulting from AFM pulling

[Robert Johnson]

Can anyone recommend a remedy/explanation for this?
Thanks,
Bob

On 9/19/07, Robert Johnson <bobjohnson1981 at gmail.com> wrote:
> Hello everyone,
> Eventually I want to pull a carbon nanotube through water at a
> constant rate. Before I get to this, I'm pulling a nanotube in vacuum
> just to make sure I'm using the pull code correctly.
>
> My system consists of a carbon nanotube aligned along the z axis and a
> single dummy atom fixed on the z axis. Here is my pull.ppa file:
>
> runtype = afm
> ngroups = 1
> group_1 = nanotube
> pulldim = Y N N
> reference_group = dummy
> reftype = com
> afm_rate1 = 0.1
> afm_dir1 = 1 0 0
> afm_k1 = 100000
> afm_init1 = 2.00 2.00 4.042
>
> Here, the coordinates for afm_init1 is the initial center of mass of
> the nanotube (thus, the system should start out with zero applied
> force). Applying this pulling force results in the nanotube undergoing
> a complicated oscillation as it moves along the +x direction. A graph
> of the nanotube position as a function of time is shown here:
> http://dept.physics.upenn.edu/~robertjo/gmx/nt-position.jpg
>
> What is causing oscillations of this type? I was expecting the
> nanotube to move at a constant rate. Does this have anything to do
> with the fact that I'm pulling the nanotube in vacuum? Perhaps in
> aqueous solution, the solvent will damp these types of oscillations.
> Any ideas as to how to remove this?
> Thanks,
> Bob
>