[gmx-users] 'constraints' directive and water

[Mark Abraham]

I amended some of the docs to clarify.

https://gerrit.gromacs.org/#/c/7728/

Mark

On Tue, Mar 27, 2018 at 9:35 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
> I'm not trying to unnecessarily extend the thread or be sarcastic - it's
> worth clarifying the situation for others and point out that you *did*
> use one of those conditions, perhaps without knowing it.
>
> #ifndef FLEXIBLE means "if you did not define FLEXIBLE, then use SETTLE"
> and you did precisely that - by not using "define = -DFLEXIBLE," you
> satisfied the condition. That's the default behavior because all of the
> force fields built into GROMACS were parametrized for use with a rigid
> water model, so we sort of take that decision out of the hands of the user.
>
> -Justin
>
> On 3/27/18 3:31 PM, Alex wrote:
> > I never ever used either, but I totally agree that sarcasm was
> > warranted. :)
> >
> > Alex
> >
> >
> > On 3/27/2018 1:28 PM, Justin Lemkul wrote:
> >>
> >> Yeah, the distinction between "ifndef" and "ifdef" can easily be
> >> missed :)
> >>
> >> -Justin
> >>
> >> On 3/27/18 3:26 PM, Alex wrote:
> >>> Yes, perfect. From my previous post, you can see that I simply got
> >>> confused by the syntax of definitions.
> >>>
> >>> Thanks a bunch.
> >>>
> >>> Alex
> >>>
> >>>
> >>> On 3/27/2018 1:21 PM, Justin Lemkul wrote:
> >>>>
> >>>>
> >>>> On 3/27/18 3:18 PM, Alex wrote:
> >>>>> That was always my default impression, but from looking into e.g.
> >>>>> tip4p.itp i somehow got the idea that water _is_ affected by
> >>>>> 'constraints'.
> >>>>>
> >>>>
> >>>> In case this is confusing for anyone else, let me explain:
> >>>>
> >>>> There is a difference between [settles] and [constraints].
> >>>> [settles] are always on unless you use "define = -DFLEXIBLE" in the
> >>>> .mdp file. When "constraints = none" is specified, the only
> >>>> explicit bond constraints (that are not SETTLE) that get used are
> >>>> those listed in [constraints] directives. So, while SETTLE is a
> >>>> constraint method, it's not subject to the "constraints" keyword in
> >>>> the same way.
> >>>>
> >>>> -Justin
> >>>>
> >>>>> Yes, whenever I have hydrogens in the system (aside from water), I
> >>>>> always set 'h-bonds', which, if you recall my old 'meh' regarding
> >>>>> constraints, suggests that I have accepted your view for
> >>>>> computational efficiency. :) This certainly answers my question,
> >>>>> thank you.
> >>>>>
> >>>>> Alex
> >>>>>
> >>>>>
> >>>>> On 3/27/2018 1:11 PM, Justin Lemkul wrote:
> >>>>>>
> >>>>>>
> >>>>>> On 3/27/18 3:10 PM, Alex wrote:
> >>>>>>> Hi all,
> >>>>>>>
> >>>>>>> Some of my simulations run with a time step of 2 fs and
> >>>>>>> 'constraints' set to 'none'. Everything runs perfectly fine, but
> >>>>>>> with such a time step, do you usually set constraints to
> >>>>>>> 'h-bonds'? I know I should be looking at literature for this,
> >>>>>>> but just wanted to get a basic idea on whether people do this.
> >>>>>>>
> >>>>>>
> >>>>>> Normally constraining bonds to H is required to get stable
> >>>>>> integration with dt = 2 fs. Water is a different matter; it is
> >>>>>> held rigid with SETTLE and is not under the influence of the
> >>>>>> "constraints" keyword.
> >>>>>>
> >>>>>> -Justin
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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