[gmx-users] Constraints & Restraints

[Justin A. Lemkul]

darrellk at ece.ubc.ca wrote:
> Hi,
> I just have a quick question on contraints and restraints. My
> understanding is that "constraints" fix the position of an atom in
> space and "restraints" restrain the deviation of the atom's position
> from its equilibrium point. Is that correct? If so, then I am a little

No.  A constraint fixes the value of some property (bond length, angle).  A 
restraint indeed biases a certain property (position, distance, dihedral, etc) 
around some equilibrium value, but it is not strictly fixed.  For more, see here:

http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints

> confused by the purpose of "constraints = all-bonds" or "constraints
> = none" in an mdp file, since by selection of a force field, which has
> bond/angle/dihedral stretching/bending/torsion constants, we are
> specifying the constraints applied to the simulation. So then what is
> the purpose of "constraints = all-bonds" and "constraints = none"?
> 

See the LINCS references in the Gromacs manual for detailed descriptions of how 
constraints are used and what they're doing.

-Justin

> Thanks.
> 
> Darrell

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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