[gmx-users] Constraints & Restraints
erikm at xray.bmc.uu.se
Thu Nov 12 12:30:55 CET 2009
Mark Abraham skrev:
> 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).
Agreed. And this is especially true for hydrogen atoms as I understand
it, since their behaviour as quantum particles deviate more from a
classical treatment than is the case for heavier nuclei. This is
mentioned in the gromacs manual.
>>> 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>
>>> <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,
>>> On Wed, Nov 11, 2009 at 9:32 PM, <darrellk at ece.ubc.ca> wrote:
>>>> 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"?
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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