Thank you!
Now its crystal clear! :-)
==> Just putting everything together ...
The actual total energy, Etot, is given by:
Etot=EKtot+EPtot ,
where EKtot and EPtot are the names used in the mdout file for the kinetic
and potential energy, respectively.
The kinetic energy at a given step (i) , EKtot in the mdout file, is given
by
EKtot (i) = 1/2 sum_j ( m_j v_{a,j}^2 ),
where v_{a,j} is the jth atom's averaged velocity between i+0.5dt and
i-0.5dt.
The potential energy, EPTOT is given by
EPTOT= BOUND + ANGLE + DIHED + {Elect_int} + {VW_int},
as defined respectively in the 1st equation of page 13 of AMBER 12 manual.
In case of having a restrain (by using nmropt, e.g.) an extra term has to
be added (RESTRAINT) to get the total potential energy, EPTOT.
The first 3 terms of EPTOT: BOUND, ANGLE, DIHED are clearly explained in
p.13 AMBER12 manual, and correspond to the first 3 terms of the 1st eq. As
for the electrostatic and VW interactions, they are given by:
{Elect_int} = EELEC + 1-4 EEL
{VW_int} = VDWAALS + 1-4 NB
where the first term (in both equations) accounts for the non-"1-4"-bounded
interactions, and the second term account for the scaled contribution to
the electrostatic/VW energy arising form the 1-4-bounded terms (as nicely
explained by Brian or in here
http://archive.ambermd.org/201204/0701.html).
The scaling factor of the 1-4 interactions is given in the prmtop file
(SCEE_SCALE_FACTOR and SCNB_SCALE_FACTOR, as explained in
http://ambermd.org/formats.html#topology )
EAMBER=EKtot+BOUND + ANGLE + DIHED + {Elect_int} + {VW_int}
All the energies are in kcal/mol.
Thanks once again!
Cheers,
Guilherme
On Fri, Aug 9, 2013 at 11:15 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>
> On Aug 9, 2013, at 7:20 AM, Brian Radak <radak004.umn.edu> wrote:
>
> > 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.
>
> The velocities are averaged between t+1/2 dt and t-1/2 dt. This is
> accurate to the order of dt^2 I think. Perhaps marginally worse than
> velocity verlet, but still quite good. (And a lot better than straight
> verlet for velocities).
>
> HTH,
> Jason
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
====================================================
*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
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Received on Sat Aug 10 2013 - 07:00:04 PDT
