Maria, try this. There actually is a lot of this on the mailing list,
so I suggest checking it a little deeper for your next querry, or at
least outlining how you looked and what you found so that it is clear
you have tried.
Also, read about pull_pbcatomN and think carefully about how you want
to set that up. It is a *global* index.
; COM PULLING
pull = umbrella
pull_geometry = position
pull_dim = N N Y
pull_start = no
pull_nstxout = 500
pull_nstfout = 500
pull_ngroups = 1
pull_group0 = <<<bilayer-group>>>
pull_pbcatom0 = 0
pull_group1 = <<<pulled-group>>>
pull_pbcatom1 = 0
pull_init1 = 0 0 0.0
pull_rate1 = 0
pull_k1 = <<<force-constant>>>
pull_vec1 = 0 0 0
-- original message --
The manual does discuss restraining to a plane, but this must be the plane
in which the atom is already present.
[ position_restraints ]
; ai funct fc
...
3 1 1000 0 0
How about restraining the atom to some other plane? For example, how about
restraining a phosphate group initially at the lipid-water interface to the
bilayer center (for whatever fancy reasons) ? Won't this require pulling the
atom to that plane first?
If it can be achieved using the position restraints alone, it is not clear
to me how to do this?
-Maria
On Tue, Sep 7, 2010 at 12:53 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
maria goranovic wrote:
I want to restrain certain atoms of my simulation to the plane
perpendicular to the bilayer normal, and at the bilayer center. Can someone
please provide a quick guide on how to do this? I read the pull-code
options, but restraining to a plane did not seem possible?
You can restrain atoms to a plane using position restraints. See the
manual for an example.
-Justin
--
Maria G.
Technical University of Denmark
Copenhagen
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