[gmx-users] Gromacs Tutorial by Justin

[Justin Lemkul]

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

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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