Re: Varying Force Simulations

From: Viral D. Tejani (vdt204_at_lehigh.edu)
Date: Mon Feb 26 2007 - 02:10:47 CST

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@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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