[gmx-users] intermolecular energy

[Jones de Andrade]

Hi all.

First, I would like to apologize for the previous message. Maybe I've been
too "harsh"? Sorry for that.

Second, I would like to list all the energetic contributions for one (same
system, different run) run that g_energy allowed me to get:

Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift
-------------------------------------------------------------------------------
Bond                        2.05116  0.0591887          0  -0.123751   -
30.9381
Angle                         2.638  0.0664036          0   0.114896
28.7242
LJ (SR)                    -14.3726  0.0865671          0 -0.0877988   -
21.9499
Disper. corr.             -0.378693 0.00211843          0 -0.00185533  -
0.463837
Coulomb (SR)               0.128875  0.0164563          0 0.000956545
0.239138
Coulomb (LR)             0.00237452 4.3944e-05          0 3.95014e-05
0.00987542
Coul. recip.               -145.145   0.660423   0.652976 -0.00137031   -
0.34258
Potential                  -10.2211   0.138681          0 -0.0988822   -
24.7207
Kinetic En.                 7.67642  0.0990863  0.0988019 0.000103943
0.025986
Total Energy               -2.54473   0.167497          0 -0.0987789   -
24.6949

Temperature                  123.15     1.5896     1.5896 3.34002e-06
0.000835011

Ok, those are with nmol 500, but it doesn't seem to matter that much. If
anybody asks, I can do all them again without that.

Any help would be really thankfull!

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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