[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

[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

[gmx-users] Simulation box size, LIE and PME

Greetings The discussion list had helped me about understanding what to do when I want to calculate binding free energy using LIE after doing MD simulation using PME. Now I need your help about choosing the simulation box size for ligand and complex. I used -d 1.0 in editconf for the complex

[gmx-users] Re: Ligand simulation for LIE with PME

Greetings again If I use a salt concentration for neutralizing the protein-ligand complex and run MD using PME, and the ligand is neutral, do I perform ligand MD simulation without adding any salt concentration? It could be relevant for LIE free energy calculation if I don't include salt in ligand

[gmx-users] Reaction field zero, ions, twin-range and LIE

Hello users For making a rerun of a MD simulation done with PME, but this time using Reaction field zero, do I eliminate the ions from the system, previously added to neutralize and ran with PME? What do you think about using a twin-range cut off instead of reaction field zero? I need to obtain

[gmx-users] Re: Thankful

Justin, thank you very much for your kind help about LIE and PME Williams -- gmx-users mailing listgmx-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

[gmx-users] Re: Reaction field zero and ions

Hello If I did the MD simulation using PME and neutralized with ions, and I want to rerun this time with reaction field zero, is there any problem if I keep the ions? This is for LIE calculation. I am using AMBER99SB. Thanks Williams -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Re: ok, thank you

/plain; charset=ISO-8859-1; format=flowed On 11/11/13 12:08 PM, Williams Ernesto Miranda Delgado wrote: Hello If I did the MD simulation using PME and neutralized with ions, and I want to rerun this time with reaction field zero, is there any problem if I keep the ions? This is for LIE