Dear Elio:
First, you need to convert your PMF to a free energy difference
between states. That means defining a boundary between, for example,
bound and unbound states. The integrate your PMF over the bound and
unbound states to get two dG values, and their difference is your free
energy of binding.
Next for the standard state correction that is required to convert
this free energy of binding into a standard state free energy of
binding. This is necessary because the volume available to the unbound
state affects the dG value. In the simplest case, you are going to
calculate the concentration of your ligand in the unbound state and
make a volume-based energetic correction to the dG value to align the
dG with a 1M concentration of unbound ligand.
This may be a little more complex depending on how did your
simulations (US vs. FEP for example) but still the whole idea behind
this is that you need to report values for dG at 1M concentration of
ligand.
There may be other corrections that you require, but if you're having
trouble with this concept then you should move to a simple system for
now.
If you still have trouble, then your next post should include thinks
like "I tried this... but I didn't understand this specific part...."
to make it clear that you have put in the effort here.
Chris.
-- original message --
Hello. I was wondering if anyone could explain how to convert delta
G's from a PMF (generated by umbrella sampling and WHAM) into standard
state values? There are some posts here on how to do this, but are too
mathematical for me to figure out. I also found the same problem when
reading some papers that do standard state correction. So if anyone
has the time to explain this again in a more basic manner it would be
appreciated. Thanks.
Elio Cino
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