Hi all,
I want to calculate the free energy difference for ATP-->GTP in
solution, for the forward analysis, the parameters for free energy perturbation
are as follows:
free-energy = yes
sc-alpha = 0.3
sc-power = 1
sc-sigma = 0.25
sc-coul = no
couple-intramol = yes
init-lambda-state = $LAMBDA$
coul-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.00 1.0
1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0
vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.05 0.1
0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0
nstdhdl = 50
calc-lambda-neighbors = 1
The calculated free energy difference is about -273 kJ/mol. In order to
check the FEP convergence, backward analysis was also done. I adopt two ways to
carry out backward analysis.
(1) Modify the topology file for GTP--> ATP , the parameters of free energy
calculation is the same as forward analysis. And the free energy difference of
backward is about 213 kJ/mol.
（2）Using the same topology file as forward analysis. But modify the parameter
settings of coul-lambdas and vdw-lambdas for free energy calculation shown as
follows
free-energy = yes
sc-alpha = 0.3
sc-power = 1
sc-sigma = 0.25
sc-coul = no
couple-intramol = yes
init-lambda-state = $LAMBDA$
coul-lambdas = 1.0 0.9 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0.0 0.00 0.0
0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0
vdw-lambdas = 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.95 0.9
0.85 0.8 0.75 0.7 0.65 0.6 0.55 0.5 0.45 0.4 0.35 0.3 0.25 0.2 0.15 0.1 0.05 0.0
nstdhdl = 50
calc-lambda-neighbors = 1
The calculated free energy difference is about 272 kJ/mol
Theoretically, the two ways of backward analysis is the same. And the values of
free energy should be identical. Now, I am confused whether I misunderstand
something or set the wrong parameters for FEP calculation. Would you like to
give me some help？ Thanks in advance.
Best wishes
Duan Baogen
Beijing Computational Science Research Center
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