Hi David,<br><br>Thanks for your reply!<br><br>It is a pure ionic liquid system. I compared this energy result with that of another system, found that the term of "Coul.-recip." is very smaller (-4664.24) than another system's result (-
56014.1). All other terms of the energy are in the same order of magnitute. <br><br>What does Coul.-recip mean? <br><br>PME is used for Coulomb interaction. Switch is used for LJ interaction.<br>
<br>1. abnormal result<br>
Energy Average RMSD Fluct. Drift Tot-Drift<br>-------------------------------------------------------------------------------<br>Bond 8121.16 129.568 129.564
0.000320592 3.20592<br>Angle 16284.9 174.598 174.578 -0.00090818 -9.0818<br>Ryckaert-Bell. 4489.18 147.842 144.019 -0.0115717 -115.717<br>LJ-14 1169.97
34.0818 33.9909 -0.000861911 -8.61912<br>Coulomb-14 2666.03 191.396 186.964 -0.0141849 -141.849<br>LJ-(SR) -32381.8 146.511 146.4 -0.0019765 -19.765<br><span style="color: rgb(255, 0, 0);">
Disper.-corr. -2462.41</span> 5.29279 5.28651 8.934e-05 0.8934<br>Coulomb-(SR) -11046.1 213.609 210.484 0.0126112 126.112<br>Coul.-recip. -4664.24 141.26 136.108
0.0130948 130.948<br>Potential -17823.3 250.663 250.472 -0.00338716 -33.8716<br>Kinetic-En. 32678.4 188.545 188.545 -6.01562e-06 -0.0601562<br>Total-Energy
14855.1 163.416 163.122 -0.00339318 -33.9318<br>Temperature 299.965 1.73071 1.73071 0 0<br><br><br>2.normal results<br>Energy Average RMSD Fluct. Drift Tot-Drift
<br>-------------------------------------------------------------------------------<br>Bond 3707.66 103.252 103.238 0.000572337 5.7156<br>Angle 10644.9 157.095
157.095 4.14791e-06 0.0414228<br>Ryckaert-Bell. 3215.44 108.937 108.932 -0.000366312 -3.65815<br>LJ-14 1314.19 29.5303 29.5302 -3.01152e-05 -0.300743<br>Coulomb-14 -
14049.8 17.4104 17.4061 0.000134398 1.34216<br>LJ-(SR) -11648.8 158.786 158.35 0.00408289 40.7735<br>Disper.-corr. -1192.91 3.76608 3.73988 0.000153815 1.53606<br>
Coulomb-(SR) -31913.4 149.436 148.956 0.0041528 41.4716<br><span style="color: rgb(255, 0, 0);">Coul.-recip. -56014.1</span> 36.3764 36.0691 0.00163665 16.3442<br>Potential -
95936.8 248.465 246.67 0.0103406 103.266<br>Kinetic-En. 23457.6 186.095 186.095 1.29671e-05 0.129495<br>Total-Energy -72479.2 162.228 159.458 0.0103536 103.395<br>Temperature
399.928 3.17272 3.17272 2.21097e-07 0.00220797<br>
<br><br><br><br><div><span class="gmail_quote">2007/3/6, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Qiao Baofu wrote:<br>> Hi,<br>><br>> I have a 10 ns job. But when using the g_energy to calculate the<br>> component of the energy, I got a positive total-energy!!<br>><br>> Who can give some suggestions? Thanks a lot!
<br>><br>what kind of system? do you happen to have an organic solvent?<br>in that case you should subtract the self energy per molecule<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.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755
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