Question about the fundamentals of MD and WHAM

From: Junwoong Yoon (junwoony_at_andrew.cmu.edu)
Date: Thu Jul 19 2018 - 15:52:43 CDT

Dear NAMD users,

I am a beginner in NAMD. I have several questions about the fundamentals of
MD and WHAM. These might be trivial to you but I really want to understand
how MD and WHAM work beforehand. I already did some research to answer
these questions but it was a bit difficult to fully understand as a
beginner...

1) I want to know what does MD actually do when the colvar is off (no
external potentials) and on. Does it just determine what is the equilibrium
(lowest energy) state when colvar is off?

2) I heard that it often takes too long to find the full free energy
landscape without external bias potentials. If this is because of lack of
sampling beyond the energy barriers, what actually hinders the sampling (or
how the probability came from)? And how the low probability to sample
beyond the barrier is related to thermodynamic quantities such as free
energy, etc?

3) When we apply external bias potentials using Umbrella Sampling methods,
how will WHAM unbias them? I saw some equations that explains how it works
but could not fully understood.

I really appreciate your taking time to help others.
Best,
Jun

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