[gmx-users] Constraints & Restraints

[Mark Abraham]

Darrell Koskinen wrote:
> 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?

Actually not. It would be a better model of a harmonic potential (duh), 
but it has been shown that the use of constraints can lead to a (more?) 
acceptable model of a real system, and they allow a larger integration 
time to boot. Check out the papers for the constraint algorithms (refs 
in GROMACS manual).

Mark

>> 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
>>>