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