GROMACS version: 5.1.4
GROMACS modification: Yes/No
Dear Justin,
1- I’ve read your tutorial entitle “Free Energy of Solvation”, you didn’t active the coulombic interactions between methane and water by setting “couple-lambda0 = vdw and coul_lambdas = 0.00 0.00 0.00 …0.00”. I want to calculate the free energy of a functionalized Fullerene in water, it is true that I must use “couple-lambda0 = vdw-q” and coul_lambdas = 0.00 0.05 …1.00"???
2- How can I calculate the entropic contribution in this method?
Best regards,
Ganj
My tutorial is explicitly for the vdW transformation only as it is a reproducible quantity from a well-known published article. If you want to compute a complete free energy of solvation, you need to transform the Coulomb terms as well by setting a series of λ states for them as well.
gmx bar prints ΔG and ΔS for neighboring windows.
Dear Justin,
Many thanks, I’ll set “couple-lambda0 = vdw-q” and coul_lambdas = 0.00 0.05 …1.00" in my .mdp file. But just a question about ΔS, how can I obtain ΔS? by subtracting the summation of S_A from summation of S_B?
Best regrads,
Ganj
Presumably, but I’ve never cared about that quantity in any of the calculations I’ve done so I can’t say for sure.