@@ -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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+
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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
@@ -826,18 +834,10 @@ Choose respectively ``temperature`` (10), ``pressure`` (11) and
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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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-
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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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