Hi all.<br><br>First, I would like to apologize for the previous message. Maybe I've been too "harsh"? Sorry for that.<br><br>Second, I would like to list all the energetic contributions for one (same system, different run) run that g_energy allowed me to get:
<br><br>Energy Average RMSD Fluct. Drift Tot-Drift<br>-------------------------------------------------------------------------------<br>Bond 2.05116 0.0591887 0 -
0.123751 -30.9381<br>Angle 2.638 0.0664036 0 0.114896 28.7242<br>LJ (SR) -14.3726 0.0865671 0 -0.0877988 -21.9499<br>Disper. corr. -0.378693
0.00211843 0 -0.00185533 -0.463837<br>Coulomb (SR) 0.128875 0.0164563 0 0.000956545 0.239138<br>Coulomb (LR) 0.00237452 4.3944e-05 0 3.95014e-05 0.00987542<br>Coul. recip. -
145.145 0.660423 0.652976 -0.00137031 -0.34258<br>Potential -10.2211 0.138681 0 -0.0988822 -24.7207<br>Kinetic En. 7.67642 0.0990863 0.0988019 0.000103943 0.025986<br>
Total Energy -2.54473 0.167497 0 -0.0987789 -24.6949<br><br>Temperature 123.15 1.5896 1.5896 3.34002e-06 0.000835011<br><br>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.
<br><br>Any help would be really thankfull!<br><br>Sincerally yours,<br><br>Jones<br><br><div><span class="gmail_quote">On 6/23/07, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">
spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Jones de Andrade wrote:<br>> Hi David!<br>><br>
> Ha, so there is something extra? Thanks a lot.... :) I knew I was<br>> forgeting something.<br>><br>> So how should I deal with it? I mean, what are the contibutions that are<br>> inside the "Potential" option of g_energy? Does it include all
<br>> corrections, disp.corr. ones also, or there is something missing?<br>><br>these are inside the Coulomb LR (PME) or some other Coulomb term (RF<br>corrections).<br><br>Energy is of course the sum of all terms. Try without the nmol flag to
<br>g_energy first.<br><br>> Thanks a lot!<br>><br>> Jones<br>><br>> On 6/23/07, *David van der Spoel* < <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><br>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">
spoel@xray.bmc.uu.se</a>>> wrote:<br>><br>> Jones de Andrade wrote:<br>> > Hi Mark.<br>> ><br>> > Haven't got exactly what you said. So let me rephrase myself:<br>> >
<br>> > The CF4 molecule doesn't have dihedrals nor intramolecular LJ and<br>> > coulombic contributions.<br>> ><br>> > What kind of contribution am I missing that makes potential
<br>> energy minus<br>> > bond stretching minus angle bending *different* from Lj +<br>> coulomb(SR) +<br>> > coulomb (LR) + Disp correction?<br>> ><br>> > Thanks a lot in advance,
<br>> ><br>> > Sincerally yours,<br>> ><br>> > Jones<br>> ><br>> I didn't follow the whole discussion, but there are also exclusion<br>> corrections when using PME or RF.
<br>><br>> --<br>> David.<br>> ________________________________________________________________________<br>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>> Dept. of Cell and Molecular Biology, Uppsala University.
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</a><br><br><br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.
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