namd1 - abf analysis

From: blicebauma_at_duq.edu
Date: Thu Sep 11 2008 - 08:19:46 CDT

Hey Everybody,

I am somewhat new to using NAMD and VMD, and I am trying to use abf to
find the potential of mean force for a small alpha-helical peptide. From
the output file, how do I analyze the output data (A(xi), xi, sample,
etc.), and how many runs would be necessary to analyze the data properly?
For the time being, I am working with a 19-residue peptide called walp19.
Thanks!

Anna

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