[gmx-users] 'constraints' directive and water

[Alex]

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
>>>>>
>>>>
>>>
>>
>