[gmx-users] Comm-mode

[Amin Rouy]

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
>>>
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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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