[gmx-users] pull parameters

[Justin A. Lemkul]

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 
simulations.

-Justin

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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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