Hello I am trying to run umbrella sampling for my system. I have system with four ion pair (cation and anion) of ionic liquids and 2048 water molecules. I am trying to PMF calculation with cation-anion distance as a reaction coordinate. I choose cation as group1 and anion group2. Box dimensions are 39.222 39.222 39.222 90 90 90
Durinh equilibratation cation and anion gets dissociate and move far from each other (around 7-8 A). Both cation and anion are close to edges of the box. 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. Can I define pull_rate1 = -0.01 to get cation and anion to get close. How can I keep cation and anion at center or if they close to the box edges then does the periodic images of the system will interact? Down I pasted the part of pull code used in my.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 = -0.01 ; 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
