[gmx-users] AFM/COM Pulling differences?

C Johnson helstreak at hotmail.com
Sun Oct 24 18:20:19 CEST 2010


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

And the other is Justin's umbrella sampling tutorial using COM pulling

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?

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