Re: external force

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Nov 02 2006 - 13:55:24 CST

Have you had a look at the online tutorial?

http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix.pdf

Read the chapter about "Steered Molecular Dynamics"

It's what I used to understand how to setup my simulations.

Hope this helped.

Best,

   Gianluca

On Thu, 2 Nov 2006, Al-Rawi, Ahlam wrote:

> Dear All,
> Could I get your help please.
> I have a system that contain B-sheet formed by two proteins in solution.
> I need to apply external force to pull away the two proteins that form the B-sheet.
> I read the on-line document, but I am not sure that I understand what kind of changes I need to do and where in the pdb file and the configuration file.
> Thank
> Ahlam
>
> Ahlam Al-Rawi
> Physics Department
> Kansas State University
> 785-532-5520
> cell 785-317-5858
>
>
>

-----------------------------------------------------
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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