AMBER Archive (2007)

Subject: Re: AMBER: NAB MD Output

From: Russell Brown (Russ.Brown_at_Sun.COM)
Date: Mon May 07 2007 - 18:06:27 CDT

Hi. I am the author of the most recent version of the NAB force field
calculations, including the energy and its first and second derivatives.
  I adopted the printout conventions of earlier versions of NAB.

"ff" means the force field energies that are printed out every ntpr
iterations (see p. 101 of the NAB User's Manual). "Total" is the total
internal energy. "bad" is the sum of the 1-2, 1-3 and 1-4 bonded
energies. "VdW" is the Van der Waals energy. "elect." is the Coulombic
or electrostatic energy. Offhand, I don't know what "cons." means.
"genBorn" is the generalized Born energy. No, the electrostatic energy
is not incorporated into the generalized Born energy. The generalized
Born energy has both electrostatic and non-polar components, but these
components are distinct and different from the VdW and Coulombic energy.
  You may see where all of these energies are calculated by examining
the mme34() function of the eff.c source code file.

"md" means the energies that are printed out every ntpr_md iterations
(see p. 102 of the NAB User's Manual). The first column is the
iteration. The second column is the time step. The third column is the
kinetic energy. The fourth column is the potential energy. The fifth
column is the sum of the kinetic and potential energies. The sixth
column is the temperature. I agree that the "md" output doesn't match
up and in fact would benefit from its own set of column headings, but
those would interfere with the "ff" column headings. If you have a
suggestion for improving this output, I could probably implement it.
You may see where all of these energies are calculated by examining the
md() function of the sff.c source code file.

Russ Brown

adelene_at_Stanford.EDU wrote On 05/07/07 03:30 PM,:
> 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?
>
> Thanks!
>
> Adelene
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