Dear Gmx Users, I run SMD to extract the windows for US calculations. The system involves negatively charged ligand and protein. I generated the protein-ligand complex within self assembly MD simulations.
I pulled my molecule away and two ions were also detached from the protein surface being attached to my ligand. My question: if I run my US caluclation and combine windows by WHAM (I specified in my umbrella.mdp my ligand as a pull_group1 and same protein residues I pulled it from as pull_group0) will get the PMF profile for my ligand binding or ligand and two ions binding? Steven -- 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
