Kinetic energy is handled the same as in standard md. One the forces are
set up in neb (as you described) then the MD part proceeds with integrating
those forces as usual. Note that there is no force from the kinetic energy,
otherwise you are correct.
On Mon, Jan 20, 2020, 3:25 PM SHAUNAK BADANI <
shaunak.badani.research.iiit.ac.in> wrote:
> Dear Amber users,
>
> I am a beginner and I want to run NEB simulations for alanine dipeptide. I
> was going through the tutorial on amber website and the related research
> papers.
>
> My question is regarding the implementation of NEB with simulated
> annealing. So, at the any point of time at any image, there is a force at
> each atom due to its kinetic energy, potential energy (decoupled to
> consider just perpendicular component) and spring force (decoupled to
> consider just parallel component). It is not clear to me how the
> contribution of kinetic energy is handled during NEB minimization to make
> sure it doesn't affect convergence. Any help would be highly appreciated.
>
> Regards,
> Shaunak Badani
> 3rd year Undergraduate,
> IIIT Hyderabad
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Received on Mon Jan 20 2020 - 14:00:01 PST
