[gmx-users] Free energy: sum or average

[VITALY V. CHABAN]

>From the context - yes. But when integrated, the result is unphysical, a
big number. In turn, when averaged, the result is comparable to the
experiment.

*Maybe the output in dgdl.xvg is already an integral, not what is written??*





On Sun, Mar 13, 2016 at 4:10 PM, Szilárd Páll <pall.szilard at gmail.com>
wrote:

> On Sun, Mar 13, 2016 at 7:18 PM, VITALY V. CHABAN <vvchaban at gmail.com>
> wrote:
>
>> Upon free energy calculations via continuous decoupling,
>>
>> free-energy              = yes
>> couple-moltype           = MOL
>> couple-lambda0           = vdw-q
>> couple-lambda1           = none
>> couple-intramol          = no
>> init-lambda              = 1.0
>> delta-lambda             = -4e-8
>> sc-alpha                 = 1.0
>> sc-power                 = 1.0
>> sc-sigma                 = 0.3
>>
>>
>> *should dG/d(lambla) be integrated or averaged to get the free energy
>> difference between lambda=1 and lambda=0? *
>>
>
> The former, but I'd use BAR.
>
> You may want to check out the literature and/or tutorials like the ones on
> e.g. www.alchemistry.org.
>
> --
> Szilárd
>
>
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>