Dear Amber community,
I'm trying Accelerated Molecular Dynamics (dual boost, amd=3) on my
system. I want to calculate (corrected) free energy surfaces for certain
pairs of coordinates.
According to what I've read, the reweighting procedure consists of
obtaining the histogram with the following equation
Hij = \sum_k \delta_ij Exp(\beta*\DeltaV)
where the sum is over all the frames k, \delta_ij is 0 if the frame "k" the
coordinates in question fall into bin (ij) and cero otherwise, \beta is
1/kT and \DeltaV is the biasing potential.
The problem is, the manual doesn't explain how to read the amd.log file.
What's the meaning of each of the nine columns of the amd.log file?
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Received on Tue Apr 16 2013 - 15:00:04 PDT
