[gmx-users] AFM/COM Pulling differences?

Justin A. Lemkul jalemkul at vt.edu
Sun Oct 24 19:04:44 CEST 2010

C Johnson wrote:
>>/ 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
> /
> I'd like to be able to have a single peptide with the N-terminus anchored and pull the C-terminus with constant
> velocity so that a force vs displacement plot could be generated.

You can do that with any of the pulling methods except "constant_force," which, 
per its name, is not a constant velocity pulling method :)  The outputs you will 
get are force vs. time and displacement vs. time, but you can post-process that 
to get the plot you want.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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