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

[hagop demirdjian]

Hi all,

I am currently trying to get familiar with FEP and want to study a box 
of 256 water molecules with annihilation of one water.

I built the following topology file using the manual template, but 
whatever are the parameters for "type B  charge" in the [atoms] section, 
the value of dH/dlambda is 0.000 in dgdl.xvg

--------------------------------------------------------------------
[ defaults ]
; nbfunc	comb-rule	gen-pairs 
fudgeLJ 
fudgeQQ
   1		1 
	no		1.0	1.0

[ atomtypes ]
;name        mass      charge   ptype            c6           c12
    OW    15.99940       0.000       A   0.26171E-02   0.26331E-05
    HW     1.00800       0.000       A   0.00000E+00   0.00000E+00

[ moleculetype ]
; molname	nrexcl
spc-water 
	1

[ 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


[constraints]
;  atom_1  atom_2  function distance_1-2	distance B
	1	2 
	1 	0.1
	1	3 
	1 	0.1
	2 	3 	2 	0.16333

[ exclusions ]
1 
2 
3 

2 
1 
3 

3 
1 
2


[ system ]
vanishing water

[ molecules ]
spc-water   256
_________________________________________________________________________________

the commands in my .mdp files are :

free_energy         =  yes			
init_lambda         =  0.50  			
delta_lambda        =  0.0



I noticed that if I introduce a "distance B" in the [constraints] 
section, which is the procedure for constraint force computation, then I 
get values for dEpot/dlambda.

I am using the most recent version of GROMACS.

Any help ?

Thank you,
Hagop