Dear Gromacs users,
I am trying to compute the free energy of hydration of ethane in order to get
more familiar with the implementation of expanded ensemble in Gromacs v. 4.6.1.
The simulations runs fine and the balancing/weight factors are equilibrated
after around 1.6 ns (a short equilibration time but this should be ok for a
rough estimate of dG).
After this the simulation is continued for another 14 ns. At the end I look at
the balancing factors to get a fast estimate of dG and see that they are tiny:
MC-lambda information
N CoulL VdwL Count G(in kT) dG(in kT)
1 0.000 0.000 16290 0.00000 -0.09268
2 0.200 0.000 14940 -0.09268 -0.01647
3 0.500 0.000 14627 -0.10914 -0.03867 <<
4 1.000 0.000 14080 -0.14781 0.02986
5 1.000 0.200 14309 -0.11795 0.07408
6 1.000 0.400 15170 -0.04386 0.01711
7 1.000 0.600 15276 -0.02675 -0.02304
8 1.000 0.800 15061 -0.04979 -0.06110
9 1.000 1.000 14328 -0.11090 0.00000
When adding these to get dG they value is way off what I get if I use the more
traditional approach of separate simulations at each lambda value and using BAR
at the end.
Does anyone have any ideas why I get these values?
Here is my mdp-file:
integrator = sd
tinit = 0
dt = 0.001
nsteps = 15000000
comm-mode = Linear
nstcomm = 10
nstlog = 1000
nstenergy = 100
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.0
cutoff-scheme = verlet
coulombtype = PME
rcoulomb = 1.0
vdw-type = cutoff
rvdw = 1.0
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-04
DispCorr = EnerPres
tc-grps = System
tau_t = 5.0
ref_t = 300
Pcoupl = berendsen
tau_p = 10.0
compressibility = 4.5e-5
ref_p = 1.013
gen_vel = no
constraints = all-bonds
constraint-algorithm = lincs
; Free energy/expanded ensemble
free-energy = expanded
sc-alpha = 0.5
sc-r-power = 6
init-lambda-state = 0
coul-lambdas = 0.0 0.2 0.5 1.0 1.0 1.0 1.0 1.0 1.0
vdw-lambdas = 0.0 0.0 0.0 0.0 0.2 0.4 0.6 0.8 1.0
calc-lambda-neighbors = 9
nstdhdl = 200
dhdl-print-energy = yes
couple-moltype = C1X
couple-lambda0 = vdw-q
couple-lambda1 = none
couple-intramol = no
nstexpanded = 100
lmc-stats = wang-landau
lmc-move = metropolis
lmc-weights-equil = wl-delta
weight-equil-wl-delta = 0.001
wl-scale = 0.7
wl-ratio = 0.8
init-wl-delta = 1.0
wl-oneovert = yes
Thanks in advance!
/ Joakim--
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