[gmx-users] Gromacs Tutorial by Justin

[Faezeh Pousaneh]

Thank you.


Best regards


On Wed, Mar 7, 2018 at 1:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/7/18 6:24 AM, Faezeh Pousaneh wrote:
>
>> Dear Justin,
>>
>> I have 2 questions regarding your tutorial on Carbon Dioxide in this link:
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
>> -tutorials/vsites/index.html
>>
>> 1- I see that in your simple simulation you use no boundary conditions,
>> pbc=no, should it be always so for this model?
>>
>> 2- You use
>>   comm-mode = angular,
>> is that necessary?
>>
>
> The simulation is a simple gas-phase system, which does not use PBC and
> hence requires angular COM motion removal.
>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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> jalemkul at vt.edu | (540) 231-3129
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