**From:** Jérôme Hénin (*jhenin_at_ifr88.cnrs-mrs.fr*)

**Date:** Wed Jan 05 2011 - 07:39:37 CST

**Next message:**JC Gumbart: "RE: NAG simulation problem with CPS"**Previous message:**Jérôme Hénin: "Re: .colvars.state file in ABF"**In reply to:**BIN ZHANG: "free energy perturbation"**Next in thread:**Jérôme Hénin: "Re: free energy perturbation"**Maybe reply:**Jérôme Hénin: "Re: free energy perturbation"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi Bin,

The sentence is slightly ambiguous. What it means is this:

The convergence analysis requires "backwards" energy differences.

Suppose we have three lambda-points, a, b, and c. The forward

calculation gives us samples of deltaU_ab at point a and deltaU_bc at

point b. For convergence analysis, we need a histogram of deltaU_ba

sampled at point b, which we don't have. That is the job of the

backwards calculation. (In the old linear paradigm, that was not

necessary because there was a simple, linear relationship between

deltaU_ba and deltaU_bc).

So while it is true that the free energy difference can be computed

from a one-way run, the two-way calculation is needed for more

elaborate analyses (which include overlap sampling and Bennett's

acceptance ratio method).

Cheers,

Jerome

On 5 January 2011 09:07, BIN ZHANG <zhngbn_at_gmail.com> wrote:

*> Hi, All:
*

*> I have a question about on comment in the FEP tutorial (Page 14), which I
*

*> quote as following:
*

*> " Since a soft-core potential [12, 13] has been introduced to avoid the
*

*> so-called “end-point catastrophes”, the potential energy no longer varies
*

*> linearly with the coupling parameter . It is, therefore, necessary that the
*

*> reverse transformation be carried out explicitly to access G+!, as is
*

*> proposed in the above NAMD scripts."
*

*> I do not fully understand the logic here. Why the reverse transformation has
*

*> to be carried out to access the dG in nonlinear case? One should be able to
*

*> calculate the energy difference, which is needed to calculate dG, in either
*

*> case.
*

*> Any input is greatly appreciated.
*

*> Best,
*

*> Bin
*

*>
*

**Next message:**JC Gumbart: "RE: NAG simulation problem with CPS"**Previous message:**Jérôme Hénin: "Re: .colvars.state file in ABF"**In reply to:**BIN ZHANG: "free energy perturbation"**Next in thread:**Jérôme Hénin: "Re: free energy perturbation"**Maybe reply:**Jérôme Hénin: "Re: free energy perturbation"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Wed Feb 29 2012 - 15:56:31 CST
*