Re: Varying Force Simulations

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Mon Feb 26 2007 - 14:52:35 CST

Viral,

Bear in mind that a MD simulation is a single molecule experiment. The
bond breaking in wet lab experiments is a statistical event which is
probably difficult to reproduce in a single simulation where you are
varying the force. I think it's better to run multiple simulations at
different constant forces if you want to probe the energy landscape and
compare to experiments.

You might have already had a look at the following paper:

Thomas, W.E., Trintchina, E., Forero, M., Vogel, V., and Sokurenko, E.V.
(2002) Bacterial adhesion to target cells enhanced by shear force. Cell
109: 913-923.

Gianluca

On Mon, 26 Feb 2007, Viral D. Tejani wrote:

> Gianluca,
>
> Thank you for your suggestion.
>
> The reason I want to apply a varying force is to test out a relation determined in
> Evans' "Probing the relation between force - lifetime - and chemistry in single
> molecular bonds," where he empirically determined that the critical force at which a
> bond breaks is linearly proportional to the natural log of the Loading Rate.  The
> loading rate is the slope of a linear function of force over time.
>
> Thus, I would need to apply a variable force over a period of time to obtain a
> loading rate.
>
> If anyone has another suggestion, please let me know.  Your help is appreciated.
>
> - Viral
>
> Gianluca Interlandi wrote:
>
> I don't think there is such a parameter in NAMD. But what you could do is
> to restart the simulation from the restart files and use every time a
> different (larger) force.
>
> BTW, Why do you want to do that? I don't know what you are doing and you
> might be doing the right thing. But if I'm allowed to give a personal
> advice, I would rather start different independent simulations at
> different constant forces. In my opinion this is more realistic than
> manually ramping the force, because AFM experiments are performed either
> at constant force or constant velocity. But I might be wrong there.
>
> Best,
>
> Gianluca
>
> On Sat, 24 Feb 2007, Viral D. Tejani wrote:
>
>
>
> Hi,
>
> I am an undergraduate Chemical Engineering major at Lehigh University in
> Bethlehem, PA.
>
> I am performing research that involves NAMD / VMD, where I am working with an
> integrin/collagen complex. I want to perform a simulation where I can apply a
> varying force over time. I have done constant force and constant velocity
> simulations by modifying files as show in the NAMD Tutorial. However, the
> tutorial make no reference to how to apply a varying force on a molecule.
>
> Is such a thing possible with NAMD? If so, how can I modify my files to add a
> parameter for varying force?
>
> Any help is appreciated.
>
> - Viral
>
>
>
>
> -----------------------------------------------------
> Dr. Gianluca Interlandi gianluca_at_u.washington.edu
> +1 (206) 685 4435
> +1 (206) 714 4303
> http://biocroma.unizh.ch/gianluca/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
>
>
>
>

-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
                    +1 (206) 685 4435
                    +1 (206) 714 4303
                    http://biocroma.unizh.ch/gianluca/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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