Re: combine PMF/dual FEP -> correct free energies?

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Fri Dec 12 2008 - 11:10:14 CST

Dear Sebastian,

As far as I can see, your plan should work. It is probably worth
looking at some binding free energy calculation papers from Benoît
Roux's group. They are the biggest players in that field.

Incidentally, thank you for replying (indirectly) to my "poll" on
conformational free energy calculations. So far you're the only one.

Jerome

On Thu, Dec 11, 2008 at 8:09 PM, Sebastian Stolzenberg
<s.stolzenberg_at_gmail.com> wrote:
> Dear Jerome, Dear All,
>
> I need to do some free energy calculations with restraints. To get a correct
> free energy value, I decided to separate my calculations into three parts:
>
> a) gradually add a few positional restraints (PMF module with 'slow growth -
> up')
> b) dual-topology transformation (alchemical FEP module) c) gradually
> release positional restraints (PMF module with 'slow growth - down')
>
> Sum of all 3 free energy differences=total free energy difference
> To maintain the final restraints from a) in b), I will simply impose a
> tclSCript with exactly the same force constants and equilibrium distances.
>
> Does this combination of PMF/dual FEP work in practice to obtain reasonable
> free energies? If no, what other options should I consider instead?
>
> Thank you,
> Best,
> Sebastian
>
>

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