[gmx-users] lambda value for free energy calculation

[kordzadeh at aut.ac.ir]

Hi Dr.Abraham 

Thank you very much for your answer 

excuse me but, I didn't understand

I want to calculate free energy of drug in water and I want to consider VDW,coulombic and bonding interation with these lambda value

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

I think I don't need mass , temperature and restraint value , however I don't know application of them exactly

probably when temperature and mass change ,we use those lambda value and when we have a restraint in system we use restraint  lambda value.

excuse me for elementary question

I'm beginner with Gromacs

Thank you very  much for your help

Regards

Azadeh

 

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