[gmx-users] 'constraints' directive and water
jalemkul at vt.edu
Tue Mar 27 21:21:32 CEST 2018
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
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.
> 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.
> 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"
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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