[gmx-users] Explaination of some terminology

[Dallas Warren]

Proper dihedrals deal with rotation around a bond i.e. for a chain
C-C-C-C, the proper dihedral will encodes the potential energy versus
angle curve for the rotation around the central -C-C- bond.

>From the GROMACS Manual
http://manual.gromacs.org/current/reference-manual/functions/bonded-interactions.html#improper-dihedrals:

4.2.12 Improper dihedrals
Improper dihedrals are meant to keep planar groups (e.g. aromatic
rings) planar, or to prevent molecules from flipping over to their
mirror images, see Fig. 4.8.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.




On Wed, 29 May 2019 at 11:07, Anh Vo <atv55 at msstate.edu> 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?
>
>
> Thank you very much.
>
>
> Best,
>
> Anh Vo
> --
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