[gmx-users] intermolecular energy

[David van der Spoel]

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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