[gmx-users] RE:Free energy methods Protein-Protein

lloyd riggs lloyd.riggs at gmx.ch
Mon Oct 17 14:40:16 CEST 2011

Dear All,

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.

The paper:
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...

Freundlishen Grüsse

Stephan Watkins
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