On 10/20/14 6:16 AM, RINU KHATTRI wrote:
hello gromacs users i am working on protein complex with popc membrane i want to calculate the free energy of complex i have run protein complex and dppc tutorial how to start for that i am using 4.5 version of gromacs should i use GROMACS Tutorial Free Energy Calculations: Methane in Water kindly help
Your question is ill-defined. Free energy of what? If you're looking for free energy of ligand binding, the fact that the protein is in the membrane is of little practical difference to any other protein-ligand complex. Compute a full thermodynamic cycle in the binding site, and one in water, and take the difference.
The methane-in-water example is the basic idea, and discusses the process for full cycles on ligand systems, but doesn't illustrate it explicitly. There's tons of literature on this topic, though.
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