[gmx-users] position restraint on a plane

[Justin A. Lemkul]

Quoting Myunggi Yi <myunggi at gmail.com>:

> Thank you.
>
> I've already read the part, but I was wondering how can I supply my
> reference z positon in the .itp file.

You don't.  If you read the link that was provided earlier, or the manual, as
has been suggested, you will find that posre.itp does not contain coordinate
information; it supplies force constant information.  Again, refer here:

http://wiki.gromacs.org/index.php/Position_Restraints

-Justin

>
> I can prepare the "restraint.gro" file manually by placing the atoms at z=
> 1.0 nm.
> Then I think I can supply with -r option.
>
> Have a great day.
>
>
> On Jan 16, 2008 3:44 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>
> > Myunggi Yi wrote:
> > > Thank you.
> > >
> > > I'm a beginner.
> > > How can I setup the restrain?
> > > Where should I get the information.
> > > The manual is not enough for me.
> >
> > There's even an example of planar restraints in chapter 5.
> >
> > > The position restraint .itp file dosen't seem to offer for the reference
> > > (z= 1.0) option.
> > > Whould give me more detail?
> >
> > You're not constraining to a plane, you're restraining the coordinates
> > to be near the plane it starts on (but for advanced usage read about
> > grompp -r). For now, see the links on the URL that Anirban provided.
> >
> > Mark
> > _______________________________________________
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>
>
>
> --
> Best wishes,
>
> MYUNGGI YI
> ==================================
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> Institute of Molecular Biophysics
> Florida State University
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>
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>



========================================

Justin A. Lemkul
Graduate Research Assistant
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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