[gmx-users] 'constraints' directive and water
nedomacho at gmail.com
Tue Mar 27 21:26:12 CEST 2018
Yes, perfect. From my previous post, you can see that I simply got
confused by the syntax of definitions.
Thanks a bunch.
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
> 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.
>> 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.
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