[gmx-users] Free energy pertubation

[Alessandra Villa]

> Citando Alessandra Villa <A.Villa at chem.rug.nl>:
> 
> > 
> > Hi, 
> > 
> > did you put free_energy=yes and delta_lambda not equal to zero? 
> Yes.
> 
> > 
> > Are the LJ parameters or the charges of state A  different from the one 
> > of state B? 
>  I want them to be, but I don't know exactly how to do this: I want to "grow"
> the molecules from zero LJ/charge parameters to their full value, so they are
> slowly inserted in the membrane interior.



So in your *ipt file you have something like this :

;   nr   type  resnr residue  atom   cgnr     charge       mass  typeB
chargeB      massB
    1    DUM      1    dum   C65     10       0.0    12.011   C   0.000
12.011 


where DUM is an atom with zero LJ/charge parameters 

and 
does it work? 
did you look what the log file says?

 


>   
> Thank you for your reply, Alessandra.
> 
> Regards,
> 
> Pedro.
> 
> --
> Pedro Alexandre Lapido Loureiro
> Laboratório de Física Biológica
> Instituto de Biofísica
> UFRJ
> Brasil 
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