Re: FEP triangular bracket average

From: Mert Gür (gurmert_at_gmail.com)
Date: Sat Apr 26 2008 - 15:26:21 CDT

Ok thanks for the hint,
I will check it out.
Mert

On 4/26/08, Jerome Henin <jhenin_at_cmm.chem.upenn.edu> wrote:
>
> Mert,
> The NAMD user's guide has a chapter on alchemical FEP that goes into
> more detail than the tutorial on some points. I think you can find the
> information you need there.
> Jerome
>
>
> On Sat, Apr 26, 2008 at 2:14 PM, Mert Gür <gurmert_at_gmail.com> wrote:
> > Thanks a lot,
> > So NAMD does perform a single simulation for state A (or the hybrid
> > structure?) and evaluates the potential energies using a hybrid
> structure.
> > For both cases I have a question
> > 1-If NAMD performs the simulation for state A ,how does it decide which
> > hybrid structure configurations correspond to the configurations of
> state A.
> > 2-If NAMD performs the simulation for the hybrid structure, why does
> this
> > simulation represent the average in state A but not in B.
> > Best regards,
> > Mert
> >
> >
> >
> >
> >
> > On 4/26/08, Jerome Henin <jhenin_at_cmm.chem.upenn.edu> wrote:
> > > Mert,
> > >
> > > As you say, no combination of energy values sampled from independent
> > > simulations in states A and B will give you the average in state A
> > > that is needed for FEP.
> > >
> > > Instead, to evaluate the FEP average, both energy functions A and B
> > > (or at least their difference) should be computed on-the-fly during a
> > > single simulation in state A. The alchemical free energy feature of
> > > NAMD does just that. Calculation of both potential energy functions is
> > > made possible by providing a "hybrid" topology that describes two
> > > chemical systems at once.
> > >
> > > Best,
> > > Jerome
> > >
> > > On Sat, Apr 26, 2008 at 6:56 AM, Mert Gür <gurmert_at_gmail.com> wrote:
> > > > Dear all,
> > > >
> > > > I have a problem understanding the theory of free energy
> perturbation
> > > > method. I have read several papers and have also read the alchemical
> > free
> > > > energy perturbation tutorial.
> > > >
> > > > As explained very simply at this link:
> > > >
> > > > http://en.wikipedia.org/wiki/Free_energy_perturbation
> > > >
> > > > the triangular brackets denote an average over a simulation run for
> > state A.
> > > > In practice, one runs a normal simulation for state A, but each time
> a
> > new
> > > > configuration is accepted, the energy for state B is also computed.
> > > > Let say I have run a simulation for state A in NAMD and a simulation
> for
> > > > state B in NAMD.
> > > > I now have energy values for each snapshot of A and B. So I actually
> > have
> > > > the distribution (probability) function for A and B seperately.
> > > > If I havent understand it wrong, MD already gives me the Boltzman
> > > > distribution so that I have just to take the simple average (sum/N)
> of
> > any
> > > > property I have recorded at N snapshots. By doing so I have the
> > triangular
> > > > bracket average.
> > > > How do I perform the same for <E(A)-E(B)>A (definition given in the
> > link).
> > > > I mean do I simply subtract each energy value I record at each
> snapshot
> > for
> > > > B, from the energy value I recorded for A.
> > > > If I do so I dont see how it becomes the average over a simulation
> run
> > for
> > > > state A.
> > > >
> > > > Thanks in advance,
> > > >
> > > > Mert Gur
> > > > Computational Science and Engineering
> > > > Koc University
> > > > Istanbul/Turkey
> > >
> >
> >
>

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