[gmx-users] intermolecular energy

[Jones de Andrade]

Hi David.

Just tried it, and it isn't getting not even funny!

Ok, without using the nmol flag, calculated total, potential and kinetic
energy.

Results:

Potential                  -5109.46    69.1951     68.569   0.128686
32.1718
Kinetic En.                 3838.21    67.9417    67.9418 -9.04753e-05  -
0.022619
Total Energy               -1271.25    96.7844    96.3384   0.128594
32.1488

As all can see: The total energy doesn't appear from the simple sum of
kinetic and potential.

I'm not expecting this to be a bug. But I'm not quite getting what am I
forgeting. What kind of contribution can be lacking where?

Thanks a lot in advance,

Sincerally yours,

Jones

On 6/23/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Jones de Andrade wrote:
> > Hi David!
> >
> > Ha, so there is something extra? Thanks a lot.... :)   I knew I was
> > forgeting something.
> >
> > So how should I deal with it? I mean, what are the contibutions that are
> > inside the "Potential" option of g_energy? Does it include all
> > corrections, disp.corr. ones also, or there is something missing?
> >
> these are inside the Coulomb LR (PME) or some other Coulomb term (RF
> corrections).
>
> Energy is of course the sum of all terms. Try without the nmol flag to
> g_energy first.
>
> > Thanks a lot!
> >
> > Jones
> >
> > On 6/23/07, *David van der Spoel* < spoel at xray.bmc.uu.se
> > <mailto:spoel at xray.bmc.uu.se>> wrote:
> >
> >     Jones de Andrade wrote:
> >      > Hi Mark.
> >      >
> >      > Haven't got exactly what you said. So let me rephrase myself:
> >      >
> >      > The CF4 molecule doesn't have dihedrals nor intramolecular LJ and
> >      > coulombic contributions.
> >      >
> >      > What kind of contribution am I missing that makes potential
> >     energy minus
> >      > bond stretching minus angle bending *different* from Lj +
> >     coulomb(SR) +
> >      > coulomb (LR) + Disp correction?
> >      >
> >      > Thanks a lot in advance,
> >      >
> >      > Sincerally yours,
> >      >
> >      > Jones
> >      >
> >     I didn't follow the whole discussion, but there are also exclusion
> >     corrections when using PME or RF.
> >
> >     --
> >     David.
> >
> ________________________________________________________________________
> >     David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> >     Dept. of Cell and Molecular Biology, Uppsala University.
> >     Husargatan 3, Box 596,          75124 Uppsala, Sweden
> >     phone:  46 18 471 4205          fax: 46 18 511 755
> >     spoel at xray.bmc.uu.se
> >     <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
> >     <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
> >
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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