[gmx-users] RE:Free energy methods Protein-Protein
lloyd.riggs at gmx.ch
Mon Oct 17 14:40:16 CEST 2011
I tried to post this once before. In any case;
Basically I am doing free energies quickly, and then plan on doing pull runs. This former is simply EQ all the way to NPT (700-1000 PS +), then a 5 PS run for the bound, then unbound system. Energy differences are taken as the difference between averidges for the entire final run (ie a single number not a graph) Basically, I woundered according to the paper listed below, if anyone knows of a rule of thumb for how many replicates a person should do to publish which represents the entire distribution of calculated Free energies (total) and for pull runs to satisfy reviewiers? I asume around 20 or so.
Biophys J. 2008 October 15; 95(8): 3575–3590.
Protein-Protein Interaction Investigated by Steered Molecular Dynamics: The TCR-pMHC Complex, Michel A. Cuendet and Olivier Michielin
The publication does each one around 157 times (ie 157 individual, unique starting point trajectories).
My other questions, are if anyone has pointers, suggestions or critiques, etc...
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