[gmx-users] free_energy = yes & init_lambda = 0.00 does not yield identical energies to free_energy = no.

[Chris Neale]

Hello,

when applying the free energy code, I expected that the instantaneous 
energy of a given conformation when free_energy = yes & init_lambda = 
0.00 would be identical to that when free_energy = no. However, I have 
found this not to be the case in zero-step mdrun. This is the same 
result that I get from gmx v 3.3.1, 3.3.3, and 4.0.3. Is this expected?

With free_energy = yes & init_lambda = 0.00:
Coulomb (SR)    -3.23064e+05

With free_energy = no:
Coulomb (SR)    -3.22654e+05

and all other energy components are identical. The Coulomb (SR) 
difference seems significant to me. Note that the free_energy = no 
values are identical to those that I get when I use a topology that has 
not been modified to add a B-state so I don't think that my A-state 
values are incorrect.

## free_energy related .mdp options:
free_energy              = yes
init_lambda              = 0.00
delta_lambda             = 0
sc_alpha                 =0.0
sc-power                 =1.0
sc-sigma                 = 0.3

## Other .mdp options:
nsteps              = 0
tinit               =  0
dt                  =  0.004
integrator          =  sd
comm_mode           =  linear
nstcomm             =  1
comm_grps           =  System
nstlog              =  2500
nstlist             =  5
ns_type             =  grid
pbc                 =  xyz
coulombtype         =  PME
rcoulomb            =  0.9
fourierspacing      =  0.12
pme_order           =  4
vdwtype             =  cut-off
rvdw_switch         =  0
rvdw                =  1.4
rlist               =  0.9
DispCorr            =  EnerPres
Pcoupl              =  Berendsen
pcoupltype          =  isotropic
compressibility     =  4.5e-5
ref_p               =  1.
tau_p               =  4.0
tcoupl              =  Berendsen
tc_grps             =  System
tau_t               =  0.1       
ref_t               =  300.      
annealing           =  no
gen_vel             =  no
unconstrained-start =  yes
gen_temp            =  300.
gen_seed            =  9896
constraints         =  all-bonds
constraint_algorithm=  lincs
lincs-iter          =  1
lincs-order         =  6


Thank you,
Chris.