[gmx-users] all-bonds constraints

[Justin Lemkul]

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 | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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