Hi David.<br><br>Just tried it, and it isn't getting not even funny!<br><br>Ok, without using the nmol flag, calculated total, potential and kinetic energy.<br><br>Results:<br><br>Potential -5109.46
69.1951 68.569 0.128686 32.1718<br>Kinetic En. 3838.21 67.9417 67.9418 -9.04753e-05 -0.022619<br>Total Energy -1271.25 96.7844 96.3384 0.128594 32.1488<br><br>As all can see: The total energy doesn't appear from the simple sum of kinetic and potential.
<br><br>I'm not expecting this to be a bug. But I'm not quite getting what am I forgeting. What kind of contribution can be lacking where?<br><br>Thanks a lot in advance,<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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