How reliable is the average structure of trajectory from gromacs simulation

06 June 2014 1 8K Report

While taking the average structure from GROMACS simulations of a complex, which average structure is reliable? For example in GROMACS there are three options ox (average), oq(bfactor) and q(eiwit).

Among these three which one is highly reliable? When I check these three options for my complex the bfactor and eiwit matches with the trajectory, however the average structure does not match with the trajectory (ie, the ligand is moving away from the coordinating residues.

Euzébio Guimaraes Barbosa

I usually use the Molecular Dynamics Tool of UCSF Chimera.

You may cluster the conformations and use a representative frame.

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