From: Jason Swails <>
Date: Fri, 29 Jul 2016 20:43:05 -0400

On Fri, Jul 29, 2016 at 4:40 PM, Thakur, Abhishek <> wrote:

> Hi Jason,
> Just now said that
> If you want to use your aMD trajectories for MM/PBSA, you will need to
> reweight the energy time series the same way you reweight other time series
> data coming from aMD.
> So after aMD I have not done any reweighing stuff for my analysis stuff.
> For analysis like H-bonding, PCA, RMSD, RMSF and even for clustering is it
> necessary to do reweighing for aMD?
> Can you suggest me some paper where I can find how to reweigh aMD stuff?

​The original aMD paper describes how to reweight the aMD trajectories (the
Amber manual should have this citation). You need to know the boost
energies at each of those time steps.​

cpptraj will do this reweighting for you, I believe, if you supply an aMD
data file with the boost energies corresponding to the trajectories.


Jason M. Swails
AMBER mailing list
Received on Fri Jul 29 2016 - 18:00:02 PDT
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