[gmx-users] position restraint on a plane

[Xavier Periole]

On Wed, 16 Jan 2008 16:12:23 -0500
  "Justin A. Lemkul" <jalemkul at vt.edu> wrote:
> 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.

There are no direct way to restrain an atom to stay a a particular
value in one direction (in a plan). However the solution you propose
could actually work. You might need to use small force constants at
the beginning, all the atoms won't be in the plan in the reference
structure and forcing them to move may be a problem.
The posre.itp should contain the list of the atoms with the three
(x,y,z) force constant you want to use. The details are indeed in the
manual.

good luck.

> 
> 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
>> ==================================
>> KLB 419
>> Institute of Molecular Biophysics
>> Florida State University
>> Tallahassee, FL 32306
>>
>> Office: (850) 645-1334
>> http://www.scs.fsu.edu/~myunggi
>>
> 
> 
> 
> ========================================
> 
> 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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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------