[gmx-users] question about energy fluctuation
Qiao Baofu
qiaobf at gmail.com
Thu Nov 9 16:39:51 CET 2006
I did again two group of tests, as follows. But I don't know how to submit
a bugzilla.
Test 1.
g_energy -f md3.edr
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Bond 1370.47 64.952 64.8116 0.0295732
14.7866
Angle 3541.69 99.9164 99.9059 0.0100593
5.02964
LJ-(SR) -3601.66 151.232 131.574 -0.516572 -
258.287
Coulomb-(SR) -10883 143.406 134.139 -0.351347 -175.674
Potential -30962.9 304.081 265.607 -1.0257 -
512.85
Total-Energy -22436.1 287.863 245.635 -1.03989 -
519.945
g_energy -nmol 115 -f md3.edr
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Bond 11.9171 0.5648 0 0.0295732
14.7866
Angle 30.7973 0.868838 0 0.0100593
5.02964
LJ-(SR) -3601.66 151.232 131.574 -0.516572 -
258.287
Coulomb-(SR) -10883 143.406 134.139 -0.351347 -175.674
Potential -269.242 2.64418 0 -1.0257 -
512.85
Total-Energy -22436.1 287.863 245.635 -1.03989 -
519.945
Test 2.
g_energy -f md3.edr
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Bond 27255.4 288.517 287.731 0.147486
73.7433
Angle 30206.8 299.196 299.151 -0.0361126 -
18.0563
LJ-(SR) -27021.1 1153.88 1015.89 -3.7911 -
1895.55
Coulomb-(SR) -116585 1327.11 1120.39 -4.92805 -2464.03
Potential -271448 2889.94 2444.54 -10.6792 -
5339.61
Total-Energy -183054 2912.13 2478.91 -10.588 -
5293.99
g_energy -nmol 981 -f md3.edr
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Bond 27.7833 0.294105 0 0.147486
73.7433
Angle 30.7919 0.304991 0 -0.0361126 -
18.0563
LJ-(SR) -27021.1 1153.88 1015.89 -3.7911 -
1895.55
Coulomb-(SR) -116585 1327.11 1120.39 -4.92805 -2464.03
Potential -276.705 2.94591 0 -10.6792 -
5339.61
Total-Energy -183054 2912.13 2478.91 -10.588 -5293.99
2006/11/9, David van der Spoel <spoel at xray.bmc.uu.se>:
>
> Qiao Baofu wrote:
> > Thanks.
> >
> >
> >
> > but the g_energy -nmol can only give the Bond,Angle data divided by the
> > nmol, for the Proper-Dih. LJ, Coulomb, Potential, Total-Energy, g_energy
> > -nmol 981 gives the same result as without -nmol 981, in which 981 is
> > the number of molecules.
> >
> > I am using Gromacs 3.3.1.
> >
> If this is reproducible then please submit a bugzilla.
>
> --
> 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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