Page 13 of the manual is probably supposed to cover this, but I agree that
there are a few sneaky things and "gotchas" in mdout files. I'm not at all
an AMBER code expert, so this may not be 100% accurate:
Etot = EKtot + EPtot - total energy
EKtot = 1/2 sum_i m_i v_i^2 - total kinetic energy
EPtot - total potential energy
NB: Because of Leapfrog Verlet, the velocities and positions are NEVER
propagated to the same point in time. Therefore the kinetic energy never
corresponds to an actually realized velocity vector of the system. I
believe the solution in AMBER is to either average the velocities from a
half step back and a half step forward or else somehow do a half step
integration to get EKtot. This also results in EPtot not corresponding to
the configurations written to mdcrd unless each and every integration step
is written to disk.
BOND, ANGLE, and DIHED are the exact terms specified on p. 13
The non-bond (NB) energy on p. 13 is divided into EELEC and VDWAALS which
are further divided into 1-4 (1-4 EEL and 1-4 NB respectively) and non-1-4
interactions. 1-2 and 1-3 interactions are always 0. 1-4 interactions are
scaled by fraction less than 1 that I can't remember at the moment. Note
that EELEC terms include both direct space and reciprocal space terms if an
Ewald summation method is in use.
As far as I know, no currently recommended force fields have retained
EHBOND terms. RESTRAINT includes all "ntr" and "nmropt" energy terms that
have been specified.
Any other terms that you see must be turned on explicitly. If you can't
figure out what they are, then you probably shouldn't be using those
options.
Regards,
Brian
P.S. It has always been unclear to me what is done with isotropic
long-range corrections to VDWAALS terms. I believe these are included, but
I've never been able to full understand the code for it. I would expect
this is added in to the non-1-4 sum.
On Fri, Aug 9, 2013 at 6:23 AM, José Guilherme Vilhena Albuquerque d'Orey <
guilhermevilhena.gmail.com> wrote:
> Dear developers,
>
> I was looking for the definition of each energy term printed in the mdout
> (Etot, EKtot,EPtot, 1-4 EEL, ...), e.g. how to relate some of this terms to
> the equation on page 13 of amber12 manual. Nevertheless I was not able to
> find a clear answer (not even in the mailing list).
>
> I know that the names are more or less self explanatory. Nevertheless it
> would be of great help if you could please point me to a place (web-page,
> pdf ...), where each of the energy terms appearing in the mdout file are
> briefly explained. Just in order to avoid a misunderstanding.
>
> Much obliged for your attention!
> All the best,
> Guilherme Vilhena
>
> --
> ====================================================
> *Guilherme Vilhena, Ph.D*
>
> Universidad Autonoma de Madrid,
> Departamento de Fisica Teorica de la Materia Condensada
> Facultad de Ciencias, Modulo C-5
> E-28049 Madrid, Spain
>
> tel: +34 91 497 2789
> fax: +34-91-4974950
> ====================================================
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
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Received on Fri Aug 09 2013 - 07:30:03 PDT
