GROMACS version: 2025
Hello all,
I’ve been trying to calculate the activity coefficient of methanol water mixture at specific compositions. I learned how to do TI with Martini but now I have an all-atom system not a coarse-grained model. And I have been having trouble about what methodology to follow, or which mdp file I should use etc. My workflow so far is:
1- Label one of the methanol molecules residue as something else and define it to be the coupled/decoupled molecule.
2- Add that molecule to the topology file
3- Using the same non-bonded interactions add the part about free energy to the mdp file. I am also having trouble about how to select the lambda values, I was recommended 20 states going something like this:
vdw-lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10 0.20 0.30 0.40 0.50 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
coul-lambdas = 0.00 0.20 0.40 0.60 0.80 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
4- Running a short equilibration and using gmx bar to gather the data.
5- Doing all of these for a pure methanol system to have the reference state data.
Rest is just hand calculation to find activity coefficient. Is this a correct approach? If not, can someone refer me to an article or a tutorial where I can learn the procedure from? I searched for some but couldn’t find any. I’d greatly appreciate all the help.
Best regards,