Dear all,
I have obtained a 2D PMF plot by Reweighting my GaMD calculations. The
plots show particularly 2 low energy distributions located at 2 different
locations. We suspect it to be the active and inactive form of the protein
under our studies. But since I am a beginner, I am confused as to how we
could proceed forward from this point. Firstly the low energy structure
spread over a range of 2-3 RMSD and 5-8 RMSD in the X axis. Similarly in
the Y axis too. So how could I obtain the exact 3D structures corresponding
to these Minima regions from the trajectory? Is there any way to obtain the
frame numbers during the reweighting? Could someone guide me the
methodology of the same. My main concern is that the pmf-c2-parameters.dat
has 3 columns with reaction coordinates and pmf values. From these, it is
difficult to trace back as these are not absolute coordinate values instead
the bin values. How to proceed in such situations? Kindly suggest. Any
other comments regarding the analysis part would be really helpful.
Regards,
Sruthi
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Received on Mon Apr 12 2021 - 04:00:02 PDT
