[gmx-users] 'constraints' directive and water

[Justin Lemkul]

I'm not trying to unnecessarily extend the thread or be sarcastic - it's 
worth clarifying the situation for others and point out that you *did* 
use one of those conditions, perhaps without knowing it.

#ifndef FLEXIBLE means "if you did not define FLEXIBLE, then use SETTLE" 
and you did precisely that - by not using "define = -DFLEXIBLE," you 
satisfied the condition. That's the default behavior because all of the 
force fields built into GROMACS were parametrized for use with a rigid 
water model, so we sort of take that decision out of the hands of the user.

-Justin

On 3/27/18 3:31 PM, Alex wrote:
> 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
>>>>>>
>>>>>
>>>>
>>>
>>
>

-- 
==================================================

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
http://www.thelemkullab.com

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