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

[maria goranovic]

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
>>
>>
> --
> ========================================
>
> 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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-- 
Maria G.
Technical University of Denmark
Copenhagen
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