# [gmx-users] protonation free energy: parameter setting

Udaya Dahal dahal.udaya at gmail.com
Sun Jun 2 15:55:08 CEST 2019

```Hi Everyone,

I am trying to estimate the protonation free energy using TI. My
thermodynamic cycle is :
a) VDW0 Q0 --> VDW1 Q0
b) VDW1 Q0 --> VDW1 Q1

I put varying lambda for "vdw_lambdas" and zeros for all "coul_lambdas" for
step *a* and  "vdw_lambdas=1" and varying "coul_lambdas" for step *b*. My
confusion is about the *couple-lambda0* and *couple-lambda1*. I used
"couple-lambda0 = vdw" in step *a* and "couple-lambda0 = q" in step *b*.
Do I need to put vdw for "couple-lambda1" for the step *b* mentioned above
?
Following is the free energy parameter for step b.

couple-lambda0           = q
couple-lambda1           = none
couple-intramol          = no
init-lambda              = -1
init_lambda_state        = 0
delta_lambda             = 0
nstdhdl                  = 10
fep-lambdas              =
mass_lambdas             = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
coul_lambdas             = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
vdw_lambdas              = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
bonded_lambdas           = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
restraint_lambdas        = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
temperature_lambdas      = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00

Thank you,
```