Re: Varying Force Simulations

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Sun Feb 25 2007 - 23:35:56 CST

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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