[gmx-users] Comm-mode

[Amin Rouy]

Ahan, thanks Justin. Is it default in all versions of  Gromacs?

On Mon, Mar 12, 2018 at 2:44 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/12/18 9:31 AM, Mark Abraham wrote:
>
>> Hi,
>>
>> Very many things are often simplified when you make a tutorial. Those .mdp
>> files are already complicated enough for a beginner.
>>
>
> Indeed, and comm-mode = linear is the default behavior, so it works just
> fine without bothering the user to think about such abstract concepts :)
>
> -Justin
>
>
> Mark
>>
>> On Mon, Mar 12, 2018 at 2:26 PM Amin Rouy <aminrou1986 at gmail.com> wrote:
>>
>> But, why in some Gromacs tutorial there is no comm-mode used in .mdp file,
>>> for example in 'Lysozyme in water';
>>>
>>>
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
>>> -tutorials/lysozyme/index.html
>>>
>>> On Mon, Mar 12, 2018 at 1:50 PM, Mark Abraham <mark.j.abraham at gmail.com>
>>> wrote:
>>>
>>> Hi,
>>>>
>>>> If you get this wrong, the equipartition of energy is usually broken and
>>>> the simulation is probably unphysical.
>>>>
>>>> Mark
>>>>
>>>> On Mon, Mar 12, 2018, 13:47 Amin Rouy <aminrou1986 at gmail.com> wrote:
>>>>
>>>> Dear Justin,
>>>>>
>>>>> If we do not use comm-mode, which quantity might be changed after
>>>>> simulations?
>>>>>
>>>>> Can we remove center of mass after the simulation done?
>>>>>
>>>>> On Sat, Mar 10, 2018 at 6:36 PM, Amin Rouy <aminrou1986 at gmail.com>
>>>>>
>>>> wrote:
>>>>
>>>>> thank you so much.
>>>>>>
>>>>>> On Sat, Mar 10, 2018 at 6:33 PM, Justin Lemkul <jalemkul at vt.edu>
>>>>>>
>>>>> wrote:
>>>>
>>>>>
>>>>>>> On 3/10/18 12:31 PM, Amin Rouy wrote:
>>>>>>>
>>>>>>> Thank you Justin.
>>>>>>>> What if we do not know the phase of the final result? of if we are
>>>>>>>>
>>>>>>> in 2
>>>>
>>>>> phase region (gas-liquid)
>>>>>>>>
>>>>>>>> If you're applying PBC you have to use linear as your comm-mode
>>>>>>>
>>>>>> (grompp
>>>>
>>>>> will fail otherwise, so that's a pretty good hint).
>>>>>>>
>>>>>>> -Justin
>>>>>>>
>>>>>>>
>>>>>>> On Sat, Mar 10, 2018 at 6:25 PM, Justin Lemkul <jalemkul at vt.edu>
>>>>>>>
>>>>>> wrote:
>>>>
>>>>>
>>>>>>>> On 3/10/18 12:17 PM, Amin Rouy wrote:
>>>>>>>>>
>>>>>>>>> Dear Gromacs people,
>>>>>>>>>
>>>>>>>>>> I have a question please.
>>>>>>>>>>
>>>>>>>>>> In which condition we must use center of mass removal? Is that
>>>>>>>>>> optional or
>>>>>>>>>> necessary?
>>>>>>>>>>
>>>>>>>>>> Typically necessary.
>>>>>>>>>>
>>>>>>>>> and how to know which mode (linear or angular) is better for our
>>>>>>>>>
>>>>>>>>> simulations?
>>>>>>>>>>
>>>>>>>>>> Linear is only for condensed-phase systems, angular is only for
>>>>>>>>>>
>>>>>>>>> vacuum
>>>>>
>>>>>> simulations.
>>>>>>>>>
>>>>>>>>> -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.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>>>>>>>
>>>>>>>>> ==================================================
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>>>>>>> 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.biochem.vt.edu/people/faculty/JustinLemkul.html
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> --
> ==================================================
>
> 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.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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