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updated tutorial 1
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docs/sphinx/source/tutorials/tutorial1/bulk-solution.rst

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@@ -812,6 +812,14 @@ command 3 consecutive times:
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Choose respectively ``temperature`` (10), ``pressure`` (11) and
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``density`` (16).
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The results show that the temperature remains well controlled during the NPT
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run, and that the fluid density was initially too small, i.e.,
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:math:`\rho \approx 600\,\mathrm{kg}/\mathrm{m}^3`. Due to the change in
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volume induced by the barostat, the fluid density gently reaches its equilibrium
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value of about :math:`1000\,\mathrm{kg}/\mathrm{m}^3` after a few tens of
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pico-seconds. Once the system has reached its equilibrium density, the
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pressure stabilizes itself near the desired value of 1 bar.
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.. figure:: figures/npt-T-p-rho.png
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:alt: Gromacs tutorial : NPT equilibration
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:class: only-light
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pressure, :math:`p` (b), and fluid density, :math:`\rho` (c) as a
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function of the time during the :math:`NpT` equilibration.
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The results show that the temperature remains well
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controlled during the NPT run, and
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that the fluid density was initially too small,
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i.e. :math:`\rho \approx 600\,\mathrm{kg}/\mathrm{m}^3`.
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Due to the change in volume induced by the barostat, the fluid density
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gently reaches its equilibrium value of about :math:`1000\,\mathrm{kg}/\mathrm{m}^3`
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after approximately 40 pico-seconds. Once the system has reached its equilibrium
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density, the pressure stabilizes itself near the desired value of 1 bar.
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The pressure curve reveals large oscillations in the pressure, with the pressure alternating between large negative
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values and large positive values. These large oscillations are typical in molecular dynamics, and not a source of
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concern here.
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The pressure curve reveals large oscillations in the pressure, with the
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pressure alternating between large negative values and large positive values.
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These large oscillations are typical in molecular dynamics and are not a
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source of concern here.
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Production run
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==============

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