Hi,
I would like to compute some properties derived from charge density on one or more snapshots from molecular dynamics trajectories by performing QM calculations.
Since computing these properties on a single structure might be meaningless, I was thinking in performing a clustering analysis using ptraj, pick a representative structure from each cluster and compute the QM properties on each of those representative structures.
Then, my problem is how to combine the QM results from all the snapshots to get a single result, for example a single interaction energy that then I can compare with binding affinity experimental data.
Would it be possible to weight the results from each representative structure by its Boltzman weight?
Or should I just average the results?
I know that the best way of taking into account the Boltzman distribution would be to take a very large number of independent snapshots from trajectory just like in MM-PBSA but, since the QM calulations are too expensive I only can take a small number of frames, so I would need a way to explicitly compute the Boltzman weights.
Any help would be appreciated.
Thanks in advance
Emilio
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Received on Tue Apr 07 2015 - 12:00:02 PDT
