[gmx-users] 'constraints' directive and water

[Alex]

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
>>>
>>
>