Heating a system or applying force with some function of timestep in simulation

From: Kartikey Pandey (kartikeypandey.met18_at_itbhu.ac.in)
Date: Sun Jul 17 2022 - 22:35:05 CDT

I was studying a simulation on free convection of proteins over a heated
flat plate.
As an initial idea, I thought that the convective buoyant forces acting on
our protein will be some function of thermal gradient.
And if we look at our system closely we will see that the surrounding
temperature of protein will change as some non-linear function of time.

So I had 2 questions
A) Can we heat or cool our system in NAMD, with some function of timestep?
Similarly can we apply non-constant forces on every atom? (In the tutorial,
I saw only the application of constant force using TclForces)

B) Is there any way this (convection) can be simplified. Or can it be
understood in a different way?


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