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

[Maik Goette]

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 <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
>>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> .
>