Hi David, Thanks for your reply!
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. What does Coul.-recip mean? PME is used for Coulomb interaction. Switch is used for LJ interaction. 1. abnormal result Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Bond 8121.16 129.568 129.564 0.000320592 3.20592 Angle 16284.9 174.598 174.578 -0.00090818 - 9.0818 Ryckaert-Bell. 4489.18 147.842 144.019 -0.0115717 -115.717 LJ-14 1169.97 34.0818 33.9909 -0.000861911 - 8.61912 Coulomb-14 2666.03 191.396 186.964 -0.0141849 -141.849 LJ-(SR) -32381.8 146.511 146.4 -0.0019765 - 19.765 Disper.-corr. -2462.41 5.29279 5.28651 8.934e-05 0.8934 Coulomb-(SR) -11046.1 213.609 210.484 0.0126112 126.112 Coul.-recip. -4664.24 141.26 136.108 0.0130948 130.948 Potential -17823.3 250.663 250.472 -0.00338716 - 33.8716 Kinetic-En. 32678.4 188.545 188.545 -6.01562e-06 - 0.0601562 Total-Energy 14855.1 163.416 163.122 -0.00339318 - 33.9318 Temperature 299.965 1.73071 1.73071 0 0 2.normal results Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Bond 3707.66 103.252 103.238 0.000572337 5.7156 Angle 10644.9 157.095 157.095 4.14791e-06 0.0414228 Ryckaert-Bell. 3215.44 108.937 108.932 -0.000366312 - 3.65815 LJ-14 1314.19 29.5303 29.5302 -3.01152e-05 - 0.300743 Coulomb-14 -14049.8 17.4104 17.4061 0.000134398 1.34216 LJ-(SR) -11648.8 158.786 158.35 0.00408289 40.7735 Disper.-corr. -1192.91 3.76608 3.73988 0.000153815 1.53606 Coulomb-(SR) -31913.4 149.436 148.956 0.0041528 41.4716 Coul.-recip. -56014.1 36.3764 36.0691 0.00163665 16.3442 Potential -95936.8 248.465 246.67 0.0103406 103.266 Kinetic-En. 23457.6 186.095 186.095 1.29671e-05 0.129495 Total-Energy -72479.2 162.228 159.458 0.0103536 103.395 Temperature 399.928 3.17272 3.17272 2.21097e-07 0.00220797 2007/3/6, David van der Spoel <[EMAIL PROTECTED]>:
Qiao Baofu wrote: > Hi, > > I have a 10 ns job. But when using the g_energy to calculate the > component of the energy, I got a positive total-energy!! > > Who can give some suggestions? Thanks a lot! > what kind of system? do you happen to have an organic solvent? in that case you should subtract the self energy per molecule -- 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] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- Sincerely yours, ********************************************** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 **********************************************
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