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
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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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