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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