[gmx-users] pull parameters

Justin A. Lemkul jalemkul at vt.edu
Sat Nov 19 19:40:44 CET 2011

ibi2010004 at iiita.ac.in wrote:
> Hello gmx_users,
> I want to pull ligand out of binding pocket of protein using a spring of
> some force constant which i will vary with each simulation and with
> varying pulling velocity.
> F=K(xspring - x ligand) using this equation.Now I am stucked up how to
> decide initial position of ligand and spring i.e.afm_init1 and afm_vec.
> Please guide me in this section.

I would suggest you upgrade to a more recent version of Gromacs and make use of 
the tutorial material available on the website.  Rather than use a Gromacs 
version from 5-6 years ago, a modern version (4.5.5) will give you better 
performance, newer features, greater stability, and significantly faster 



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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