[gmx-users] 'constraints' directive and water

[Justin Lemkul]

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

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