Dear list, I am trying to calculate the free energy for protonating a single monomer of oleic acid with the martini forcefield. This in preparation for other work, and I wanted to start by reproducing what is already done.
To do this, I have defined the following in my topology to describe the change in protonation state going from A (protonated) to state B (charged). The martini bead type needs to change as well in this process. [ atoms ] ; id typeA resnr residu atom cgnr chargeA massA typeB chargeB massB 1 P4 1 OAN COO 1 0 Qa -1 I also have this very simple mdp file for doing the transformation free_energy = yes init_lambda-state = 1 fep-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 And I am using fep-lambdas to describe the entire process. With this, I can run through grompp and mdrun with different values of init-lambda-state, but the output I get in each case is the same for each different simulation. I check this by gmx analyze -f md.xvg -ee And I always get the same value for the average. Is there something I am missing or not specifying properly? Thanks /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 [email protected].
