Re: Varying Force Simulations

From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Mon Feb 26 2007 - 03:23:43 CST

Hi Viral,

As Gianluca pointed out, NAMD does not provide a "ready-to-go" command to
apply a time-dependent force. However, the TclForces interface will allow
you to apply any kind of force you want after writing some Tcl lines of
code. Have a look at
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node33.html#SECTION00096800000000000000

However, I don't think you need it. Constant velocity should do it
(Look carefully at the definition of loading rate in E Evans and K Ritchie
Dynamic strength of molecular adhesion bonds Biophys. J. 1997 72:1541).

Marcos
PS: Mark, not all bonds are covalent bonds. Hydrogen bonds and also
"adhesion" bonds can be readily studied with classical MD.

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.
> -----------------------------------------------------
>
>
>
>

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