**From:** Jerome Henin (*jhenin_at_cmm.chem.upenn.edu*)

**Date:** Thu Oct 09 2008 - 17:49:05 CDT

**Next message:**Sebastian Stolzenberg: "Re: FEP: delta_G, memory of Hamiltonians corresponding to last G value?"**Previous message:**David A. Horita: "charmrun socket error"**In reply to:**Sebastian Stolzenberg: "FEP: delta_G, memory of Hamiltonians corresponding to last G value?"**Next in thread:**Sebastian Stolzenberg: "Re: FEP: delta_G, memory of Hamiltonians corresponding to last G value?"**Maybe reply:**Sebastian Stolzenberg: "Re: FEP: delta_G, memory of Hamiltonians corresponding to last G value?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dear Sebastian,

NAMD does not remember the deltaH values because they cannot be reused

for the next window as they are sampled from the wrong ensemble. Let

me explain this : if you go from A to B to C, then deltaG_AB is

computed based on (E_B - E_A) values, sampled in state A, whereas

deltaG_AB is computed based on (E_C - E_B) values sampled in state B.

So you can't use the distribution of E_B obtained in state A for the

second window (B->C).

As a side note: some greatly improved FEP code has been making its way

into CVS lately. If you are not afraid of compiling NAMD, you might

want to have a look.

Best,

Jerome

On Thu, Oct 9, 2008 at 3:10 PM, Sebastian Stolzenberg

<s.stolzenberg_at_gmail.com> wrote:

*> Dear All,
*

*>
*

*> in NAMD-FEP, say, I execute the command
*

*>
*

*> runFEPlist {.001 .01 .1} $numSteps
*

*>
*

*> After having calculated delta_G(.001)=G(.01)-G(.001) with exponential
*

*> averages of Hamiltonians, will NAMD "memorize" the Hamiltonians
*

*> corresponding to G(.01) when next calculating delta_G(.01)=G(.1)-G(.01)? Or
*

*> will it re-measure the Hamiltonians corresponding to G(.01) and then proceed
*

*> to calculate G(.1) and delta_G(.01)?
*

*>
*

*> Thank you,
*

*> Best,
*

*> Sebastian
*

*>
*

*>
*

**Next message:**Sebastian Stolzenberg: "Re: FEP: delta_G, memory of Hamiltonians corresponding to last G value?"**Previous message:**David A. Horita: "charmrun socket error"**In reply to:**Sebastian Stolzenberg: "FEP: delta_G, memory of Hamiltonians corresponding to last G value?"**Next in thread:**Sebastian Stolzenberg: "Re: FEP: delta_G, memory of Hamiltonians corresponding to last G value?"**Maybe reply:**Sebastian Stolzenberg: "Re: FEP: delta_G, memory of Hamiltonians corresponding to last G value?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Wed Feb 29 2012 - 15:49:57 CST
*