Tutorial-l Mailing List

From: Connie Wang (cywang_at_caltech.edu)
Date: Thu Aug 11 2011 - 20:41:14 CDT

Hi All,
    I first wanted to say that the NAMD tutorials are immensely helpful and
very much appreciated. I was going through the ABF tutorial for Methane
Hydration and noticed that the Free Energy Profile shown in the tutorial
manual shows the collective variable going from 0 to 20, with the
water-vacuum interface presumably occurring at 10 angstroms. However in the
example files and in the instructions the interface occurs at 15 angstroms,
and this is where the minimum in my free energy occurs. I wanted to
reproduce the correct location of the minimum and was wondering if my
interpretation of the tutorial was correct. In addition, I was wondering if
there is any need to use the larger range in the distance coordinate.

Thanks,
   Connie

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