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 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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