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

[chris.neale at utoronto.ca]

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
>>
>>