Hmm.....looks really strange...
What do you see in a visualization of the trajectory?
Do you see the whole tube hopping?
Or does it somehow stretch and shrink?
To me, the wells look somehow harmonic, what may be related to the
spring (constant). Maybe, try a different spring constant for testing.
Is the position you plot the com or the pull group?
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Robert Johnson wrote:
Can anyone recommend a remedy/explanation for this?
Thanks,
Bob
On 9/19/07, Robert Johnson <[EMAIL PROTECTED]> 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
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