[gmx-users] Comm-mode

Mon Mar 12 15:04:42 CET 2018

Thank you very much.

On Mar 12, 2018 14:51, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 3/12/18 9:48 AM, Amin Rouy wrote:
>
>> Ahan, thanks Justin. Is it default in all versions of  Gromacs?
>>
>
> As far as I remember, yes, but don't take my word for it. Look at
> mdout.mdp from grompp - it has the full list of every setting that's being
> used in your simulation (and also the top of md.log, though some of those
> are parsed in ways that make them harder to understand).
>
> -Justin
>
> 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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>>>>>> Gromacs Users mailing list
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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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>>> Gromacs Users mailing list
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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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