From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Jun 19 2007 - 00:02:42 CDT

I can attempt to answer but someone may correct me:

1) I'm pretty sure it would be the former, although it seems at least
in our group that people calculate it slightly differently (but I am
pretty sure both ways are equivalent). Please see some papers from
our group for more specifics on this point (I'm looking at right now
for instance Jensen et al. "Energetics of glycerol conduction through
aquaglyceroporin GlpF").

2) The PMF is a force profile where as the activation energy is the
amount of energy required to overcome the initial barrier. I do not
know if the free energy of activation is different or not. I have
never calculated a PMF myself, but one way to judge would be the size
of the activation energy. 100 kJ/mol (~25 kcal/mol) does seem a bit
large however and would likely only proceed if something else
provided the energy or a conformational change took place (for
comparison, thermal energy is only about 0.6 kcal/mol). One point I
will make is that calculating accurate PMFs requires good sampling,
so if you only ran one trajectory, it probably accumulated a large
amount of irreversible work. Additional trajectories, appropriately
averaged using Jarzynki's equality (again, papers from our group
would be most helpful), may yield a lower number.

More experienced people may feel free to chime in here. In any case,
good luck!

On Jun 18, 2007, at 11:00 PM, Sting wrote:

> Hi all:
>
> I have performed a series of SMD with a constant velocity of 10 Å/
> ns to force a ligand release from the binding pocket and try to
> reconstruct the PMF, and I have some problem as follow:
>
> 1. How to compute the works done during the process? Should it be:
> The displacement of ligand*applied Force or The displacement of the
> moving point which drag the ligand ?
>
> 2. What is the diffrence between the PMF and the Activation Energy
> as well as that between it and the Free Energy of Activation, and
> how to verify a reasonable PMF?
>
>
> I really need someone to help me. Thank you in advance!
>
>
>
>
>
> 　　　　　　　　Sting
> 　　　　　　　　stg1979_at_emails.bjut.edu.cn
> 　　　　　　　　　　2007-06-15

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