[gmx-users] lambda value for free energy calculation

[Mark Abraham]

Hi,

Did you understand why the tutorial recommended turning on VDW before
coulomb? Does that reasoning apply to other interactions?

Mark

On Tue, Jan 9, 2018 at 5:33 AM <kordzadeh at aut.ac.ir> wrote:

> Hi all
>
> I have aquestion about free energy calculation
>
> as  in tutorial be said if we want to consider coloumbic interaction we
> must define lambda as follows:
>
> vdw_lambdas = 0.00 0.05 0.10 ... 1.00 1.00 1.00 ... 1.00
>
> coul_lambdas = 0.00 0.00 0.00 ... 0.00 0.05 0.10 ... 1.00
>
> if I want to consider bonded interaction should I write:
>
> vdw_lambdas = 0.00 0.05 0.10 ... 1.00 1.00 1.00 ... 1.00  1.00 1.00 1.00
> ... 1.00
>
> coul_lambdas = 0.00 0.00 0.00 ... 0.00 0.05 0.10 ... 1.00 1.00 1.00 1.00
> ... 1.00
>
> bonded_lambdas=0.00 0.00 0.00 ... 0.00 0.00 0.00 0.00 ... 0.00 0.00 0.05
> 0.10 ... 1.00
>
> when should we consider temperature_lambdas,
> mass_lambdas,restraint_lambdas?
>
> Thank you very much for your help
>
> Regards
>
> Azadeh
>
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