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_vec1.
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.
-Justin
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
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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