[gmx-users] the problem about the calculation free energy of the toluene in water
Jinyao Wang
wangjy at ciac.jl.cn
Tue Sep 15 10:29:17 CEST 2009
hi,gmx-users
I am repeating the calculation of the toluene in water using GMX 4.0.4.
I have read the maillist about the the solvation free energy of toluene in water.
I know that the sc-power and the point lambda are very important. So I set sc-power=2 and 25 lambda points.
Now I get the free energy in vacuo is -2.85 Kj/mol, but I get the free energy in water is -2.12 Kj/mol. So the deltaG_hyd= -2.85 + 2.12 = -0.73 Kj/mol instead of -3.1 Kj/mol in manual. I don't know how to improve the free energy value in water.
This is my md-lambda088.mdp
cpp = /lib/cpp
constraints = all-bonds
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 50000
nstcomm = 1
nstxout = 25000
nstvout = 0
nstfout = 0
nstlog = 100
nstenergy = 100
nstxtcout = 1000
xtc_precision = 1000
xtc_grps = Protein
nstlist = 5
energygrps = Protein SOL
ns_type = grid
rlist = 0.9
coulombtype = Reaction-Field
epsilon_r = 78.0
rcoulomb = 1.4
rvdw = 1.4
Tcoupl = Berendsen
tc-grps = Protein SOL
ref_t = 300 300
tau_t = 0.1 0.1
Pcoupl = Berendsen
tau_p = 1.0
compressibility = 4.6e-5
ref_p = 1.0
free_energy = yes
init_lambda = 0.88
sc-alpha = 1.51
sc-power = 2.0
Jinyao Wang
wangjy at ciac.jl.cn
2009-09-15
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