[gmx-users] Pulling a ligand out of protein cavity

Justin A. Lemkul jalemkul at vt.edu
Tue May 31 15:46:30 CEST 2011

Shay Teaching wrote:
> Dear gromacs users,
> I am trying to pull a ligand out of a cavity of a membrane protein 
> (along the Z axis).
> Problem is, that with every pull settings I have tried the ligand gets 
> "stuck" on the protein's center of mass. How can I make it go all the 
> was to the bulk water?
> It always gets stuck on the COM. And I've tried using both umbrella and 
> constant force, so I'm getting the feeling that I'm missing something 
> trivial.
> Here's an example of one set of pull-parameters I tried:
> ------------------------------->
> pull             = constant_force
> pull_geometry    = distance

You can only use the distance method if the distance between pull_group0 and 
pull_group1 is constantly decreasing or increasing.  If you're moving through a 
channel, you should use the position method in conjunction with an appropriate 

> pull_dim         = N N Y
> pull_start       = yes        ; define initial COM distance > 0
> pull_ngroups   = 1
> pull_group0    = Protein

You probably need a better reference group, i.e. some subset of residues that 
forms the entrance or exit from the channel, but you may be able to get away 
with this reference group if you using a more appropriate pull_geometry, as 
suggested above.


> pull_group1    = Ligand
> ;pull_rate1    = -0.001        ; 0.01 nm per ps = 10 nm per ns
> pull_k1        = 1000           ; kJ mol^-1 nm^-2
> <------------------------------
> Can anyone help enlighten me as to what I am doing wrong?
> Thanks,
> -Shay
> P.S.
> Using gromacs 4.0.7.


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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