[gmx-users] all-bonds constraints

[Mark Abraham]

What does the GROMOS_54A7 paper say? What methods do its authors use with
it since?

Mark
On Apr 3, 2014 6:45 PM, "Juan Munoz-Garcia" <
juan.munoz-garcia at bioch.ox.ac.uk> wrote:

> Dear Justin,
>
> I'm using GROMOS_54A7, so when you say "Most of my tutorials constrain all
> bonds because it is common practice with those force fields" does it also
> apply to GROMOS_54A7?
>
> Thank you.
>
> Juan C. Munoz-Garcia, PhD
> Biomembrane Structure Unit
> University of Oxford
> South Parks Road
> Oxford OX1 3QU
> juan.munoz-garcia at bioch.ox.ac.uk<mailto:juan.munoz-garcia at bioch.ox.ac.uk>
>
>
>
> On 4/3/14, 6:20 AM, Juan Munoz-Garcia wrote:
> > Dear GROMACS users,
> >
> > I'm quite new with GROMACS. I come from using AMBER for a long time and
> after
> > doing quite a few GROMACS tutorials I've found in all of them that the
> > variable "constraints" is set to "all-bonds" even during the production
> run.
> > I'm quite surprised about this. My understanding as I learnt from AMBER
> is
> > that due to the high frequency of motion of the bonds with H atoms
> (aprox 1
> > fs timescale) those are fixed during the integration time step as this is
> > longer (usually 2 fs) than the motion frequency. However, all other
> bonds are
> > not fixed because their motions have larger timescales (of course this
> is a
> > simplification) than the integration time step. I find that constraining
> all
> > bonds is too "artificial" as the  bond length is supposed to be
> oscillating
> > between the equilibrium values given by the force field. As this is a
> quite
> > important difference compared to what I was used to in AMBER, I'd like
> you to
> > please tell me why is it "constraints = all-bonds" generally used during
> the
> > production run instead of "constraints = h-bonds" ?
> >
>
> A counterargument can be made that constraints are a better representation
> of
> bonds, but that's a larger issue :)
>
> Most of my tutorials constrain all bonds because it is common practice with
> those force fields (and I personally believe the rigid representation to
> be a
> better one); in practice, you need to treat the bonded interactions
> according to
> what the force field requires.  For AMBER or CHARMM parameter sets, that
> usually
> means "constraints = h-bonds" is more appropriate.  Just because a
> tutorial does
> something doesn't mean it's generally applicable.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu<
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
>
>
>
>
>
>
>
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