[AMBER] NEB Simulations in Amber

From: SHAUNAK BADANI <shaunak.badani.research.iiit.ac.in>
Date: Mon, 20 Jan 2020 20:25:26 +0000

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.

Shaunak Badani
3rd year Undergraduate,
IIIT Hyderabad
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Received on Mon Jan 20 2020 - 12:30:01 PST
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