[gmx-users] AFM/COM Pulling differences?

[Justin A. Lemkul]

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

-- 
========================================

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

========================================