[gmx-users] Re: LIE method with PME

Hello I performed MD simulations of several Protein-ligand complexes and solvated Ligands using PME for log range electrostatics. I want to calculate the binding free energy using the LIE method, but when using g_energy I only get Coul-SR. How can I deal with Ligand-environment long range

Re: [gmx-users] Re: LIE method with PME

If the long-range component of your electrostatics model is not decomposable by group (which it isn't), then you can't use that with LIE. See the hundreds of past threads on this topic :-) Mark On Thu, Nov 7, 2013 at 8:34 PM, Williams Ernesto Miranda Delgado wmira...@fbio.uh.cu wrote: Hello

[gmx-users] Re: LIE method with PME

Thank you Mark What do you think about making a rerun on the trajectories generated previously with PME but this time using coulombtype: cut-off? Could you suggest a cut off value? Thanks again Williams -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Re: LIE method with PME

I'd at least use RF! Use a cut-off consistent with the force field parameterization. And hope the LIE correlates with reality! Mark On Nov 7, 2013 10:39 PM, Williams Ernesto Miranda Delgado wmira...@fbio.uh.cu wrote: Thank you Mark What do you think about making a rerun on the trajectories