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 <[EMAIL PROTECTED]> 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* < [EMAIL PROTECTED]
> <mailto:[EMAIL PROTECTED]>> 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
>     [EMAIL PROTECTED]
>     <mailto:[EMAIL PROTECTED]>    [EMAIL PROTECTED]
>     <mailto:[EMAIL PROTECTED]>   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
[EMAIL PROTECTED]    [EMAIL PROTECTED]   http://folding.bmc.uu.se
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