[gmx-users] AFM/COM Pulling differences?

[C Johnson]

Hi,

I'm running Gromacs 4.0.7 and would like to pull a short peptide apart in order to study the binding forces (beta-sheet and alpha-helix structures).  I'm pretty confused as far as where to start.  I've found two tutorials:

One is listed here under "Pull code tutorial files (Berk)"  This uses a .ppt to set up an AFM pulling
https://extras.csc.fi/chem/courses/gmx2007/

And the other is Justin's umbrella sampling tutorial using COM pulling
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html

These tutorials seem to take two different approaches.

What is the difference is the two approaches?

If I wanted to pull a single peptide chain in order to analysis the secondary structure stability is there a standard or common method?

Thanks,
Joe
 		 	   		  
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