Hello I am trying to run umbrella sampling for my system. I have system with four ion pairs (4 cation and 4 anion) of ionic liquids and 1024 water molecules. I am trying to PMF calculation with cation-anion distance as a reaction coordinate. I choose cation as group1 and anion group2. I am getting the free energy around ~400 kcal. Can you tell where I am going wrong?
I have one more question, In my equilibrated strcutrue cations and anions are far from each other (around 7-8 A). I am more interested in structure where cation and anion close (around 2-4A) How can I do the PMF simulation to get this structure. I have pasted pull code used in mdp file. Nilesh ; Pull code pull = umbrella pull_geometry = distance pull_dim = Y Y Y pull_start = YES ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = EMI pull_group1 = ETS pull_init1 = 0.0 pull_rate1 = 0.001 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
