[gmx-users] restraining atoms to the plane at the bilayer center: pull code ?

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Sep 7 15:40:38 CEST 2010

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.

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?


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

More information about the gromacs.org_gmx-users mailing list