Vijayaraj wrote:
Hi,
What is the relation between pulling force and free energy of binding.
can we relate the maximum pulling force with the free energy. for
example, 2 systems has the maximum pulling force and free energy as
below from umbrella sampling and g_wham analysis,
max. force free energy
system 1 1470 42
system 2 1647 32
system 2 has higher pulling force than system 1 and the free energy
result is different from this trend.
How did you obtain the maximum force, just a single SMD trajectory? If so, I
wouldn't put a lot of faith in it necessarily. Umbrella sampling is a more
robust method than a single pull. You can use large numbers of pulling
simulations and apply Jarzynski's equation to calculate free energy, but there
are distinct caveats (although I suppose there are caveats with any method).
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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