[gmx-users] FEP

[P]

Hi all.
I'm new to gromacs, and I would be glad to get some advice from more experienced usres.
I would like to estimate the difference in free energy between two systems. 
 First system (A) consists of  DPPC membrane, TM-protein and some Zn ions 
interacting with the protein.  Second (B) has the same elements but Zn ions 
are far away from the protein (in the solvent).  Is it possible to estimate 
free energy difference between those two systems in gromacs?
I thought about using dummy atoms and slow-growth methods for free energy calculations.
  During the simulation, Zn ions from system (A) would be perturbated into dummy atoms
 (charge=0, mass = 0) and at the same time equal number of dummy atoms in the solvent 
would be perturbated to Zn atoms?  Is it possible to achieve?  
For the beginning  I tried to estimate the difference in free energy between two systems. 
1) first system consisted of two Cl- and one Zn2+ ions + solvent
2) second only solvent molecules 
During the 100 ps MD I perturbated  chare and mass of Cl and Zn 
ions to zero.  The energy values that I've obtained are wrong 960200,46.
 I'm new to gromacs so I would appreciate your help a lot.
Here are my input files (I'm using ffgmx )

--------------md.mdp-------------
pp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  md
dt                  =  0.001  
nsteps              =  100000 
nstxout             =  100000
nstvout             =  100000
nstfout             =  100000
nstlog              =  100
nstenergy           =  100
nstxtcout           =  100
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
free_energy = yes
init_lambda = 0
delta_lambda = 0.00001
sc-alpha = 1.5
sc-sigma = 0.3
....
...
....
---------------------------------------
--------ZN.itp-----------------------
[ moleculetype ]
; molname       nrexcl
ZnB              1

[ atoms ]
; id    at type res nr  residu name     at name  cg nr  charge              typeB chargeB massB
1       Zn      1       Zn              Zn       1      2     65.37000      Zn       0  0

---------------------------------------
-----------Cl.itp-----------------
[ moleculetype ]
; molname       nrexcl
ClB              1

[ atoms ]
; id    at type res nr  residu name     at name  cg nr  charge typeB chargeB massB
1       Cl      1       Cl              Cl       1      -1        35.45300   Cl  0   0

----------------------------



THANK YOU FOR HELP
All the best.
:)

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