[gmx-users] Comm-mode

[Justin Lemkul]

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

==================================================