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<p class=MsoNormal>Dear GROMACS users,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I am conducting energy minimization with an implicit
solvent, using GROMACS version 4.5.1 at double precision.<o:p></o:p></p>
<p class=MsoNormal>The minimization provides the minimal potential energy I’m
interested in, but I also wanted to see the contributions to it.<o:p></o:p></p>
<p class=MsoNormal>I therefore used g_energy_d and picked the potential energy
itself (no. 10) together with what I thought are its constituents (no. 1-9). However,
those contributions do not sum to the potential energy. There is also a term #Surf*SurfTen
(no. 30) but it is printed as zero. <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Can you explain this situation?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>The relevant part of g_energy_d’s output for a certain
example is the following:<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal># This file was created Thu Sep 16 16:51:26 2010<o:p></o:p></p>
<p class=MsoNormal># by the following command:<o:p></o:p></p>
<p class=MsoNormal># g_energy_d -s em2.tpr -f em2.edr -o
em2.potential_energy.xvg <o:p></o:p></p>
<p class=MsoNormal>#<o:p></o:p></p>
<p class=MsoNormal># g_energy_d is part of G R O M A C S:<o:p></o:p></p>
<p class=MsoNormal>#<o:p></o:p></p>
<p class=MsoNormal># GROningen Mixture of Alchemy and Childrens' Stories<o:p></o:p></p>
<p class=MsoNormal>#<o:p></o:p></p>
<p class=MsoNormal>@ title "Gromacs Energies"<o:p></o:p></p>
<p class=MsoNormal>@ xaxis label "Time (ps)"<o:p></o:p></p>
<p class=MsoNormal>@ yaxis label "(kJ/mol), (bar
nm)"<o:p></o:p></p>
<p class=MsoNormal>@TYPE xy<o:p></o:p></p>
<p class=MsoNormal>@ view 0.15, 0.15, 0.75, 0.85<o:p></o:p></p>
<p class=MsoNormal>@ legend on<o:p></o:p></p>
<p class=MsoNormal>@ legend box on<o:p></o:p></p>
<p class=MsoNormal>@ legend loctype view<o:p></o:p></p>
<p class=MsoNormal>@ legend 0.78, 0.8<o:p></o:p></p>
<p class=MsoNormal>@ legend length 2<o:p></o:p></p>
<p class=MsoNormal>@ s0 legend "Bond"<o:p></o:p></p>
<p class=MsoNormal>@ s1 legend "Angle"<o:p></o:p></p>
<p class=MsoNormal>@ s2 legend "Proper Dih."<o:p></o:p></p>
<p class=MsoNormal>@ s3 legend "Ryckaert-Bell."<o:p></o:p></p>
<p class=MsoNormal>@ s4 legend "GB Polarization"<o:p></o:p></p>
<p class=MsoNormal>@ s5 legend "LJ-14"<o:p></o:p></p>
<p class=MsoNormal>@ s6 legend "Coulomb-14"<o:p></o:p></p>
<p class=MsoNormal>@ s7 legend "LJ (SR)"<o:p></o:p></p>
<p class=MsoNormal>@ s8 legend "Coulomb (SR)"<o:p></o:p></p>
<p class=MsoNormal>@ s9 legend "Potential"<o:p></o:p></p>
<p class=MsoNormal>@ s10 legend "#Surf*SurfTen"<o:p></o:p></p>
<p class=MsoNormal> 0.000000 179.387112
1063.328043 64.818404 2220.374294 440.027560 3580.261354
12299.937527 -3164.489764 -44972.543752
-27990.380760 0.000000<o:p></o:p></p>
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