Hi gmx-users I am running a series of free-energy of solvation calculations for small molecules in water and octanol, to calculate partition coefficients.
For this, I have set up a series of lambda-points in water and in octanol, and then haves used primarily gmx bar to evaluate the results. Using gmx bar (v.5.0.4) with the following command line $ gmx bar -f md*xvg -o -oi -oh -b 100 &>FEP.dat I get for eg. ethanol in water a Delta-G of 14.33 kJ/mol (which is very close to the value (14.42 kj/mol) reported by eg. Lundborg and Lindahl in JPCB, 119, 2015, for the same combination of water model and forcefield, so that is reassuring). Then I tried the same analysis using pymbar (cloned today from git) like this: $ python alchemical_analysis.py -t 300 -p 1 -q xvg -p md -m BAR -v -s 100 &> FEP_pymbar.dat Now, I get a Delta-G of 64.235 kJ/mol, so clearly not the same as with gmx bar (and not simply a kJ vs kcal issue either I think) I feel like I am missing something fundamental since I get so different values, and would appreciate any feedback. The simulations have been run using gmx 5.0.4 with a total of 47 lambda points, and each run is 10 ns in length. I can provide mdp-files and such if needed. Cheers /PK -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
