[NAMD] Using ABF to study separation of two molecules

From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Mon Jan 23 2017 - 01:00:48 CST

Hi everyone,

I'm new to free energy calculations using NAMD but currently I'm studying
how two molecules separate.
To do so, in simulations I untwist and separate them (under normal
conditions they separate in milliseconds).
If I want to obtain the free energy through the reaction coordinate, which
is the most convenient thing to use,
ABF, metadynamics, umbrella sampling?
Also, if I want to use for example ABF, do I need to run it during a
simulation where I do this mechanism or do
I just have to sample during equilibrium steps of the molecules? If I
sample during equilibrium for a few nanoseconds
It doesn't seem natural to be able to get to the barrier, but If I simulate
during my mechanism aren't I putting external
Forces that will modify the real free energy?

Thank you very much,


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