[gmx-users] free energy perturbation : how to ?

[Alessandra Villa]

Hi Hagop, 


> 
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr     charge    type B 	charge
>       1	   OW	   1	SOL     OW      1      -0.82    OW	0.1
>       2	   HW	   1	SOL    HW1      1       0.41	HW	0.1	
>       3	   HW	   1	SOL    HW2	1       0.41	HW	0.1
>

The mass could be also perturbated, see pag 99 of the manual3.0.

With the topol.top, that you built up, you are trying to annihilate all
the water molecule and not one as I understond you want.

alessandra