On Wed, 16 Jan 2008 16:12:23 -0500
"Justin A. Lemkul" <[EMAIL PROTECTED]> wrote:
Quoting Myunggi Yi <[EMAIL PROTECTED]>:
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 <[EMAIL PROTECTED]> 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
[EMAIL PROTECTED] | (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
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