Hi, I want to use thermodynamic integration for calculating free energy of binding of ligand to its receptor protein. For that I would like to follow the two step approach: first decoupling Coulombic and then vdW interactions.
1. Shall I start with the same coordinate and topology files for both decoupling process and only vary the lambda values? Or before turning off vdW terms all charges in the topology file should set to zero? 2. The MDP files I am going to use are: MD1.mdp free_energy = yes init_lambda = 0.2 ; different values of lambda 0.0,0.1,0.2,0.3,....,1 delta_lambda = 0 foreign_lambda = 0.1 0.3 sc-alpha = 0 sc-sigma = 0 couple-moltype = Ligand couple-intramol = no couple-lambda0 = vdwq couple-lambda1 = vdw MD2.mdp free_energy = yes init_lambda = 0.2 delta_lambda = 0 foreign_lambda = 0.1 0.3 sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 couple-moltype = Ligand couple-intramol = no couple-lambda0 = vdw couple-lambda1 = none foreign_lambda: I put only neighboring lambda points. Is that OK? Or I should put all 11 lambda points 0 0.1 0.2 .... 0.9 1.0 ? If at any stage I have to increase the number of intermediate lambda states, say at 0.05 interval- then the closest lambda values will be different (like, for init_lambda = 0.2 foreign_lambda = 0.15 0.25). In that case do I have to rerun all simulations with their new foreign_lambda values? Soft-core parameters are set to zero during charge removal. Is it OK? 3. During decoupling process I want to specify the position of ligand relative to protein. For which I use pull code. But how to correct its contribution to free energy of binding? pull = umbrella pull_group0 = Ligand pull_group1 = Protein pull_rate1 = 0.0000 pull_k1 = 750 Thanks and best regards, Moutusi -- 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
