[gmx-users] Explaination of some terminology

[Benson Muite]

On 5/29/19 4:07 AM, Anh Vo wrote:
> Hi all,
>
> I'm new to GROMACS and there are some terms that I’m not very clear when
> reading GROMACS materials. I have looked them up and read more but I’m
> still confused. Please help me to clarify them.
>
>
>
>       - What is improper vs. proper dihedral?
>
>
>
>       - It is said that “If a dynamical system is ergodic, the ensemble
> average becomes equal to the time average”.
>
>         What does it means if a system is ergodic? Why does ensemble
> sampling becomes similar to time sampling if a system is ergodic?
Ensemble sampling becomes similar to time sampling because over a long 
enough time period, all points in phase space are explored by an ergodic 
system, thus instead of doing multiple simulations with the same global 
average quantities (such as total system energy), one can do one long 
simulation with the same global average quantity. Slightly more involved 
explanation at https://en.wikipedia.org/wiki/Ergodicity
>
>
> Thank you very much.
>
>
> Best,
>
> Anh Vo