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.
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