@@ -812,6 +812,14 @@ command 3 consecutive times:
812812 Choose respectively ``temperature `` (10), ``pressure `` (11) and
813813``density `` (16).
814814
815+ The results show that the temperature remains well controlled during the NPT
816+ run, and that the fluid density was initially too small, i.e.,
817+ :math: `\rho \approx 600 \,\mathrm {kg}/\mathrm {m}^3 `. Due to the change in
818+ volume induced by the barostat, the fluid density gently reaches its equilibrium
819+ value of about :math: `1000 \,\mathrm {kg}/\mathrm {m}^3 ` after a few tens of
820+ pico-seconds. Once the system has reached its equilibrium density, the
821+ pressure stabilizes itself near the desired value of 1 bar.
822+
815823.. figure :: figures/npt-T-p-rho.png
816824 :alt: Gromacs tutorial : NPT equilibration
817825 :class: only-light
@@ -826,18 +834,10 @@ Choose respectively ``temperature`` (10), ``pressure`` (11) and
826834 pressure, :math: `p` (b), and fluid density, :math: `\rho ` (c) as a
827835 function of the time during the :math: `NpT` equilibration.
828836
829- The results show that the temperature remains well
830- controlled during the NPT run, and
831- that the fluid density was initially too small,
832- i.e. :math: `\rho \approx 600 \,\mathrm {kg}/\mathrm {m}^3 `.
833- Due to the change in volume induced by the barostat, the fluid density
834- gently reaches its equilibrium value of about :math: `1000 \,\mathrm {kg}/\mathrm {m}^3 `
835- after approximately 40 pico-seconds. Once the system has reached its equilibrium
836- density, the pressure stabilizes itself near the desired value of 1 bar.
837-
838- The pressure curve reveals large oscillations in the pressure, with the pressure alternating between large negative
839- values and large positive values. These large oscillations are typical in molecular dynamics, and not a source of
840- concern here.
837+ The pressure curve reveals large oscillations in the pressure, with the
838+ pressure alternating between large negative values and large positive values.
839+ These large oscillations are typical in molecular dynamics and are not a
840+ source of concern here.
841841
842842Production run
843843==============
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