From: <adelene.Stanford.EDU>
Date: Mon, 07 May 2007 15:30:51 -0700

Hi, I'll like to know a little bit more about the output format for MD
using NAB (which I think is similar to Amber).

I get something like this in my output:
     iter Total bad vdW elect. cons. genBorn frms
ff: 0 -1254.79 391.88 -30.05 807.69 0.00 -2424.30 9.22e+00
md: 1 0.001 60.31 -1264.87 -1204.56 79.35

What does "ff" mean, and "md", and the formatting for "md" seems a
little strange - how do the numbers match up?

And what is this "Electrostatic" term? Aren't the electrostatic
energies all incorporated into the generalised Born approximation?


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Received on Wed May 09 2007 - 06:07:20 PDT
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