[gmx-users] lambda value for free energy calculation

[kordzadeh at aut.ac.ir]

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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