Based on your use of:
sc-sigma = 0.3
I wonder what happens with 4.5.3 when you set the env.var.
GMX_SCSIGMA_MIN to 0
quoting http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x
"for free-energy calculations sc-sigma now also sets the minimum
soft-core sigma (old tpr files retain the old behavior, which can be
enforced by setting the env.var. GMX_SCSIGMA_MIN to 0)"
-- original message --
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
foreign_lambda =
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-moltype =
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.
Regards,
Yan
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.
Chris.
-- 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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