[gmx-users] .ppa file

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 18 20:35:58 CET 2011

ibi2010004 at iiita.ac.in wrote:
> Hello Justin,
> I am doing project on afm simulation of protein complex.I have used em.mdp
> file for minimization.
> Now i am wondering where to use .ppa file for afm parameters.
> Can you guide me with files related to afm simulation.

The .ppa format has not been used in many years.  Versions in the 3.3.x series 
used them, but now all pull code settings are specified in the .mdp file. 
Please see the pulling/umbrella sampling tutorial on the Gromacs website.



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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