[gmx-users] Constraints & Restraints

[Tsjerk Wassenaar]

Hi Darrell,

Constraints and restraints also apply to relative positions. A bond
constraint fixes the bond to a certain distance. constraints =
all-bonds means that all bonds are to be converted to constraints,
rather than have them flexible, e.g. harmonic. Harmonic bonds are
actually more like restraints, penalizing deviations from the
equilibrium values. These equilibrium values and the 'penalty
function' are described in the force field.

Hope it helps,

Tsjerk

On Wed, Nov 11, 2009 at 9:32 PM,  <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
> 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"?
>
> Thanks.
>
> Darrell
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist