[gmx-users] question about energy and pressure

[Qiao Baofu]

Hi all,

I have some questions about the gromacs:

1. I simualted a pure small molecule system. All the simulation is ok. But
when I use g_energy to calculate the energy of bond, angle, lj, and coloumb,
it gives the following energy. The energies is much bigger, about 50-100
times bigger than the reported data.  What's wrong?

Statistics over 5000001 steps [ 0.0000 thru 5000.0000 ps ], 6 data sets

Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift
-------------------------------------------------------------------------------
Bond                        2869.13    93.6564    93.6562 0.000137548
0.687742
Angle                       7303.46     140.13     140.13 0.000189867
0.949334
Ryckaert-Bell.          3326.2    97.6245    97.6161 -0.000890977   -4.45489
LJ-(SR)                   -7616.62    138.684     138.67 -0.00138166   -
6.90831
Coulomb-(SR)        -22763.2    138.465    138.238 -0.00549019    -27.451
Potential                  -64743     219.54    219.203 -0.00842365   -
42.1182

2. I used the "isotropic!!" pressure coupling, but at the end of the .log
file (in the average section), it says:

 Pressure (bar)
   -2.64364e+01    3.71622e+01    3.00738e+00
    3.71622e+01    1.32932e+01   -2.49814e+01
    3.00738e+00   -2.49814e+01    1.61609e+01

The Pxx, Pyy, Pzz are not equal. Why?

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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