[gmx-users] AFM/COM Pulling differences?

[Justin A. Lemkul]

C Johnson wrote:
> 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?
> 

The difference is that Berk's tutorial is for old Gromacs versions (prior to 
4.0), since the pull code was completely re-written after version 3.3.3.  In 
theory, there is no difference.  Both tutorials provide a method for calculating 
PMF.

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

Maybe I don't fully understand your objective, but if you're just interested in 
secondary structure stability as a function of distance between two species, a 
slow steered MD run could accomplish that; you don't need umbrella sampling.  If 
you're trying to get free energies associated with different configurations, 
however, then getting the PMF is a suitable method.

-Justin

> Thanks,
> Joe
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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