[gmx-users] cluster analysis
feenstra at few.vu.nl
Fri Jun 17 11:49:59 CEST 2005
UCT Staff Member - Jackson wrote:
> After the cluster analysis I get 1 cluster and the time of the middle
> conformation. However, I want the lowest energy conformation in this
> cluster. Is there any way of getting this or of listing the energy of
> each of the conformations? Also is there a way of differentiating the
> conformations by frame number rather than time?
> I want to do several dynamic runs with different starting conformations
> and the pool them all together for a single cluster analysis.
Try g_energy to extact the energies from your original runs.
Alternatively, you may re-calculate them from the trajectory using mdrun
You can use trjconv on the trajectory with 'collected conformations', to
set the timestep between frames to 1 ps, that way, frame number and time
will be the same.
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