On Mon, Apr 4, 2011 at 7:45 AM, TAEJIN KIM <liquidhelium4k.yahoo.com> wrote:
> Dear Amber Users
>
>
>
> I have fundamental questions about
> Amber output file format. During energy minimization with iGb, there
> are two components of electrostatic energy, EEL and 1-4 EEL. In order
> to get the net electrostatic energy, do I need to add them?
>
Yes. The 1-4 EEL (and VDW) interactions are electrostatic interactions
between atoms located 3 bonds away from one another (i.e. that form a
dihedral bond). The reason these are separated is because the Amber force
fields, in general, apply a scaling factor to these non-bonded interactions
(sometimes, as in the Glycam force fields), this scaling factor is 1, but
Amber force fields use an electrostatic scaling factor of 1.2 and a VDW
scaling factor of 2.0 by default.
>
> Besides this, is there any tutorial
> which explains every detail of output format, such as ESURF, EELEC,
> EHBOND, EKCMT, VIRIAL, EAMBER, etc?
>
I don't know that there is a file describing each term definitively, but the
names are designed to be as helpful as possible. For instance, ESURF is the
non-polar solvation energy calculated as a proportionality constant
(surften) times the surface area; EELEC is the electrostatic energy, EHBOND
is the energy of H-Bond terms (10-12 terms as opposed to the standard 6-12
lennard jones terms, which aren't used in Amber force fields anymore), EKCMT
is (I believe) the kinetic energy of the COM translation (not quite sure
though), the VIRIAL is the calculated virial, and EAMBER Is the Amber energy
without any restraints (I think).
Hope this helps,
Jason
Thank you.
>
> TJ
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Apr 04 2011 - 09:30:08 PDT
