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" < [email protected]> wrote: > 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 [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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 < [email protected]> wrote: > 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 electrostatic interaction using gromacs? I have seen other > discussion lists but I couldn't arrive to a solution. Could you please > help me? > Thank you > Williams > > > -- > gmx-users mailing [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 electrostatic interaction using gromacs? I have seen other discussion lists but I couldn't arrive to a solution. Could you please help me? Thank you Williams -- gmx-users mailing [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
