[gmx-users] Different TI free energy values in 4.0.7 and 4.5.3
chai.yan.em at googlemail.com
Thu Apr 14 17:07:57 CEST 2011
Dear Gromacs users,
One example of my mdp files with lambda=0.5 is like the following:
integrator = md
tinit = 0
dt = 0.004
nsteps = 250000
simulation_part = 1
comm_mode = Linear
nstcomm = 10
nstlist = 2
ns_type = grid
pbc = xyz
periodic_molecules = no
rlist = 1.4
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.4
epsilon_r = 1
epsilon_rf = 1
vdw_type = cut-off
rvdw = 1.4
fourierspacing = 0.168
pmeorder = 4
ewald_rtol = 1.0e-5
ewald_geometry = 3d
optimize_fft = yes
tcoupl = v-rescale
tc-grps = ioq !ioq
tau_t = 0.1 0.1
ref_t = 298.15 298.15
pcoupl = Berendsen
Pcoupltype = Isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
constraints = all-bonds
constraint_algorithm = lincs
lincs_order = 4
lincs_iter = 1
free_energy = yes
init_lambda = 0.5
delta_lambda = 0
sc-alpha = 0.7
sc-power = 1
sc-sigma = 0.3
nstdhdl = 10
separate-dhdl-file = yes
dhdl-derivatives = yes
dh_hist_size = 0
dh_hist_spacing = 0.1
couple-lambda0 = vdw-q
couple-lambda1 = vdw-q
couple-intramol = no
The system has 1 Chloride ion with ffG43a1 force field parameter and SPC
water molecules with heavy hydrogen in a cubic box of size 3 nm. I have
sampled 21 lambda windows ranging from 0 to 1.
The values are converged by block averaging.
On Thu, Apr 14, 2011 at 3:35 PM, <chris.neale at utoronto.ca> wrote:
> Dear Yan:
> If you want to get to the bottom of this then (a) please report your mdp
> files and (b) show some evidence that your values are converged by, for
> instance, block averaging the run-time.
> -- original message --
> Dear Gromacs users,
> I got different free energy values by Thermodynamic Integration (TI) in
> Gromacs 4.0.7 and 4.5.3.
> When I calculated the hydration free energy of Chloride ion by using
> Thermodynamic Integration method, the results for the free energy of
> un-charging the Chloride ion from q=-e to 0 in SPC water are 359+/-6 kJ/mol
> in Gromacs 4.0.7 and 385 +/-6 kJ/mol in Gromacs 4.5.3, respectively.
> The literature value is 392 kJ/mol (J. Phys. Chem. 1996, 100, 1206-1215,
> Table 6), which is close to the result in Gromacs 4.5.3 but not in 4.0.7.
> As a check, Gromacs 3.3.1 gave the result as 381+/-3 kJ/mol.
> I searched the mail list and the bugzilla of Gromacs but didn't find
> explanation for this issue of version.
> Does anyone know the reason for the different TI free energy values in
> those different version of Gromacs?
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