[gmx-users] binding energy (score) of single trajectory frames

Knapp Bernhard bernhard.knapp at meduniwien.ac.at
Wed Oct 30 16:26:07 CET 2013

Hi users,

I was wondering if there is an easy and quick way to get a frame-wise 
binding energy between 2 groups of chains (chain ABC vs DE) in an 
existing trajectory. This is not indented to be an actual binding free 
energy approach but rather a rough indicator if the binding between two 
chains increases or decreases during simulation time. This should work 
like a protein/protein docking scoring function which assigns binding 
scores to single conformations. Is there a direct approach on an 
existing xtc (even if water was removed and not all steps were written)? 
Maybe like g_hbond but in addition with terms like Gvdw, Gdeformation, 
Ghydrophobic etc. Alternatively (and probably much more time and 
resource consuming), would it be possible to obtain this by the rerun 
option of mdrun (adjusted energy monitoring groups (the original setup 
was "energygrps =  protein	SOL"))?


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