[gmx-users] 'constraints' directive and water

Justin Lemkul 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 
> '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.


> 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


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