i have a gromacs system and after npt equilibration, the average preesure obtained by g_energy is 1 bar with a very low error state and low total drift. But the rmsd value given by the same g_energy function is 39. what is its significance?is this value normal? moreover, if i see the pressure.xvg file obtained from g_energy function, i can see the values of pressure changing like 23, then 7 then 50 the ....so on. is it normal and will it be right to proceed with this equilibrated system for my production run?
It's quite normal for pressure to wildly fluctuate from one simulation step to another (as you observed), especially in small systems, because pressure is macroscopic property. It's better to observe average pressure over time. If your pressure averages and stabilizes at 1 bar after equilibration, you should be fine. Also, see this:
http://www.gromacs.org/Documentation/Terminology/Pressure
Like Saša mentioned, pressure can fluctuate wildly. You could also take a look at the density of your system (you can check this with gmx energy as well). This is often less sensitive to sudden changes than the pressure.
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