[gmx-users] pressure dependence on volume.

[Mark Abraham]

On Sun, Oct 19, 2014 at 4:18 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> The averaged volume of the 1bar pressure NPT simulation over 150ns was very
> clearly 298.5 nm^3.
> But now, when I set the volume of the NVT simulation to 298.7 nm^3 by
> starting from a NPT frame that has the volume, the average was 1.2 bar with
> error estimate 0.53, over 52 ns.
>

... so, indistiguishable from a wide range true values near 1 bar. No big
surprise there. http://www.gromacs.org/Documentation/Terminology/Pressure

The same tactic also didn't work for a 300 ns NPT simulation and
> subsequently 300 ns NVT simulation. This NVT simulation pressure was
> averaged to be around 4 bar.
>
> Why starting a NVT simulation from a NPT frame with the averaged NPT volume
> didn't give the target pressure of 1 bar?


Because that expectation is unreasonable for this system size over this
time scale :-)

Mark


> On Sun, Oct 19, 2014 at 2:20 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
> > Hi Johnny,
> >
> > The density is M/V. The only parameter changing with pressure coupling is
> > V, so the density and volume are fully correlated. No surprise there.
> >
> > Cheers,
> >
> > Tsjerk
> > On Oct 19, 2014 2:27 AM, "Johnny Lu" <johnny.lu128 at gmail.com> wrote:
> >
> > > The frames with density closest to the average density also have
> volumes
> > > closest to the averaged volume.
> > >
> > > On Sat, Oct 18, 2014 at 8:18 PM, Johnny Lu <johnny.lu128 at gmail.com>
> > wrote:
> > >
> > > > I searched the energy file made by g_energy, and found that NPT
> frames
> > > > with very similar densities have very similar volume.
> > > >
> > > > So, I guess using density is same as using volume in this case.
> > > >
> > > > On Sat, Oct 18, 2014 at 9:09 AM, Johnny Lu <johnny.lu128 at gmail.com>
> > > wrote:
> > > >
> > > >> Would manually setting the box size make vacuum bubbles?
> > > >>
> > > >> On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu <johnny.lu128 at gmail.com>
> > > >> wrote:
> > > >>
> > > >>> my bad. that formula for density is wrong. But I till don't see why
> > > >>> using the same averaged density (instead of volume) for the NVT and
> > NPT
> > > >>> simulations would give a different result.
> > > >>>
> > > >>> On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu <johnny.lu128 at gmail.com
> >
> > > >>> wrote:
> > > >>>
> > > >>>> Was the density calculated by # particles /  volume ?
> > > >>>>
> > > >>>> If so, using volume (as I did), and using density would give the
> > same
> > > >>>> wrong pressure, upon transitioning from NPT to NVT.
> > > >>>>
> > > >>>
> > > >>>
> > > >>
> > > >
> > > --
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