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

Shay Teaching shay.teaching at gmail.com
Tue May 31 15:34:39 CEST 2011

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

Here's an example of one set of pull-parameters I tried:
pull             = constant_force
pull_geometry    = distance
pull_dim         = N N Y
pull_start       = yes        ; define initial COM distance > 0

pull_ngroups   = 1
pull_group0    = Protein
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?

Using gromacs 4.0.7.
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