[gmx-users] solvation free energy

[Daniele Veclani]

I'm trying to calculate the  solvation free energy of a molecule (M).
I have done:
M+water ---> dum+water

Now I have to do:
M(vacuo) --> dum(vacuo)

In this case I have a problem, in fact I find a DG = 0.00000 and within the
.xvg file there are only zeros.

Where is the problem?

I use gromacs 5.0.4 and my .mdp file (for lambda 00) is:
integrator               = sd
tinit                    = 0
dt                       = 0.002
nsteps                   = 2500000
comm_mode                = angular
nstcomm                  = 100
nstxout                  = 500
nstvout                  = 500
nstfout                  = 0
nstlog                   = 500
nstenergy                = 500
nstxout-compressed       = 0
cutoff-scheme            = group
nstlist                  = 0
ns_type                  = simple
pbc                      = no
rlist                    = 0
coulombtype              = cutoff
rcoulomb                 = 0
epsilon_r                = 1
vdwtype                  = cutoff
rvdw                     = 0
DispCorr                  = no
fourierspacing           = 0.12
pme_order                = 6
ewald_rtol               = 1e-06
epsilon_surface          = 0
tcoupl                   = berendsen
tc_grps                  = system
tau_t                    = 0.1
ref_t                    = 300
Pcoupl                   = no
tau_p                    = 1.0
compressibility          = 4.5e-05
ref_p                    = 1.0
free_energy              = yes
init_lambda_state        = 0
delta_lambda             = 0
calc_lambda_neighbors    = 1
vdw_lambdas              = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80
0.90 1.00
coul_lambdas             = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00
bonded_lambdas           = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00
restraint_lambdas        = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00
mass_lambdas             = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00
temperature_lambdas      = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00
sc-alpha                 = 0.5
sc-coul                  = no
sc-power                 = 1.0
sc-sigma                 = 0.3
couple-moltype           = QUI
couple-lambda0           = vdw

couple-lambda1           = none
couple-intramol          = no
nstdhdl                  = 10
gen_vel                  = no
constraints              = all-bonds  ; we only have C-H bonds here
constraint-algorithm     = lincs
continuation             = no
lincs-order              = 12

Best regards
Daniele Veclani.