Re: ParseFEP error with FEP in segments at different lambda schedule

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Aug 01 2018 - 05:40:22 CDT

"the error is square additive, however, so you would take the square root
of the sum of the errors when re-combining"

May I ask whether the above "sum of the errors" is a shortage for the "sum
of the square of the errors" ? If so, translating to a different albeit
related case, let me show some data (kcal/mol) from MM-GBSA rather than FEP
for the same system, so that /\A below should be understood as /\POTENTIAL
from NAMD plot/xmgrace

complex: -6335.08 with Stdev 64.24

receptor: -6358.87 with Stdev 63.93

ligand: 48.33 with Stdev 6.2

/\Abind = complex - receptor - ligand = -24.5 with Stdev 91

if the propagation of errors is treated here correctly, the whole is quite
disappointing.

Thanks a lot for checking

francesco

On Tue, Apr 10, 2018 at 2:56 PM Brian Radak <brian.radak_at_gmail.com> wrote:

> The simple solution to this is to break the simulations into two groups
> where the spacings are identical. So long as you get the directions correct
> the net free energy is just the sum of the two. Most people probably know
> this, but just to be complete, the error is square additive, however, so
> you would take the square root of the sum of the errors when re-combining--0000000000000eb2d705725d5332--

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