Hi all,
I am doing mutation of some ligands in water and inside the protein cavity as well and for that I chose a 3-step process to do that. 1st I do discharging and then switching the vdw's between the ligands and then in the 3rd step I do recharging again. For that I do need a four equilibrium ensemble. In the discharging step in water, I do have the 1st ligand equilibriated with charge and with non-charged and also the same for the 2nd ligand. Therefore whenever I have all those four equilibriated ensembles, I do mutate between them with the softcore potential (alpha=0.25, sigma=0.30). Now inside the protein cavity I also need the same four euilibriated ensemble. I performed the equilibration but the non-charged ligands are seems to me a bit unstable therefore I thought of taking only the state 0 and state 1 only for the mutation inside the cavity. I neglected the intermediates. I got somehow reasonable results. Since we know the non-equilibrium CGI should be started with the equilibrium ensemble therefore I am a bit nervous to do that. Could somebody direct me to do a better way or the strategy I am following, if it is okay for the simulation of mutation. thank you very much in advance. -- Susanta Haldar Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic. -- 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.