[email protected] 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
simulations.
-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
========================================
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