[gmx-users] MD structure analysis

larif sofiene larifsofiene at gmail.com
Wed Nov 9 17:21:03 CET 2011

After finishing a M.D simulation an ensuring that equilibration of the
protein is done in its solvent cube according to RMS, potential energy
,temperature , pressure , radius of gyration ... etc what structure should
i use for analysis ? is it the average structure of some few last
nanoseconds of the simulation , OR the structure of the last frame in
simulation, and is there any special cases where one of the two cited
structures could insight more than the other ? ( for example : for Hydrogen
bonds is the average structure more suitable for analysis than the last
frame ? ...)
Thanks :)
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