[gmx-users] g_bar for larger systems (protein-protein interaction)

Ricardo O. S. Soares rsoares at fcfrp.usp.br
Mon Feb 25 21:49:58 CET 2013

Hello dear users,

I just took a look at the new gromacs paper at Bioinformatics, and I 
noticed a new tool g_bar, which is used for free energy calculations. I 
also found a nice tutorial by Justin Lemkul. While I'm adapting the 
workflow to my system, I'd like to know from anyone with more expertise 
in this field, if this method can be successfully applied to larger 
molecules as ligands, other than small organic ligands. What is the 
effectiveness in determining a  protein-protein (300+ residues) energy 
of binding, if any?



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