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

2013-11-07 Thread Mark Abraham 
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
 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


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

2013-11-07 Thread Mark Abraham 
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 generated
 previously with PME but this time using coulombtype: cut-off? Could you
 suggest a cut off value?
 Thanks again
 Williams

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