[gmx-users] positive system total-energy
Qiao Baofu
qiaobf at gmail.com
Wed Mar 7 09:43:08 CET 2007
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 <spoel at xray.bmc.uu.se>:
>
> 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
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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--
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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