[gmx-users] Comm-mode

Mon Mar 12 14:51:18 CET 2018

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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>> --
>> ==================================================
>>
>> 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

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