[gmx-users] the difference between fixing and freezing and position restraint

[Justin A. Lemkul]

Banafsheh Mehrazma wrote:
> Hi everyone;
> 
> I wonder what's the difference between fixing and freezing and
> position restraining?
> I know how to position restrain, but I don't have any idea how we can
> fix or freeze.
> So I would be glad if you tell me exactly, how we can fix the solute
> while the solvent is not, and vice versa. :)
> 

Freezing is done via freezegrps (and related settings) in the .mdp file.  The 
positions of the frozen atoms are invariant.

Restraining simply applies a biasing potential to the atoms such that 
displacement is disfavored.  The strength of the restraint is controlled by the 
force constant in the posre.itp file.

-Justin

-- 
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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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