[gmx-users] Constraints & Restraints

Darrell Koskinen darrellk at ece.ubc.ca
Thu Nov 12 00:09:48 CET 2009

Hi Tsjerk,
So then, if I understand correctly, setting "constraints = all-bonds" is 
not as realistic as setting "constraints = none", since the latter will 
allow for flexible (e.g. harmonic) behavoir which is more realistic than 
fixing the bond to a certain distance, correct?


> Date: Wed, 11 Nov 2009 21:45:44 +0100
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] Constraints & Restraints
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> 	<8ff898150911111245u63c6aa65sa839f246343521f4 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 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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