[gmx-users] pressure dependence on volume.

[Tsjerk Wassenaar]

Hey :)

That is under the assumption that the pressure distribution is symmetric
for a given density. That's rather unlikely, though. You should probably
set the density to the average density for the pressure you want, so from
the density distribution at 1 bar.

Cheers,

Tsjerk
On Oct 18, 2014 9:06 AM, "Dr. Vitaly Chaban" <vvchaban at gmail.com> wrote:

> To achieve what you want you need to MANUALLY set the average DENSITY
> which you obtained from NPT. That is, you MANUALLY adjust box side
> length in the GRO file.
>
>
>
> Dr. Vitaly V. Chaban
>
> Виталий Витальевич ЧАБАН
>
>
> On Sat, Oct 18, 2014 at 1:47 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
> > I am trying to transit from NPT to NVT.
> > Using the averaged volume of NPT for NVT somehow didn't give me the 1 bar
> > pressure in NVT.
> > I don't know why that happened.
> >
> > Was it the difference between constant pressure and constant volume heat
> > capacity? But then, the thermostat should take care of that quite
> quickly.
> > After that, N, V, and T would be same for NPT simulation and the NVT
> > simulation... which means the pressure should be the same.
> >
> > Both the NVT and NPT uses the V-rescale thermostat, and the NPT uses
> > Berendsen barostat.
> >
> > Right now I'm selecting NPT frames with different volumes, and see if the
> > NVT simulations continuing from those frames would give me the 1 bar
> > pressure.
> >
> > On Fri, Oct 17, 2014 at 3:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >>
> >> On 10/17/14 11:49 AM, Johnny Lu wrote:
> >>
> >>> At least for real water, a 0.2% error in volume can mean the pressure
> is
> >>> ~30 bar when the target pressure is 1 bar.
> >>> http://docs.engineeringtoolbox.com/documents/309/water-density-
> >>> temperature-pressure_2.png
> >>>
> >>> On Fri, Oct 17, 2014 at 10:49 AM, Johnny Lu <johnny.lu128 at gmail.com>
> >>> wrote:
> >>>
> >>>  Hi.
> >>>>
> >>>> Mainly TIP3P water, 300K. The pressure is near 1 bar.
> >>>>
> >>>> A less than 1% error in volume would cause how much error in average
> >>>> pressure?
> >>>>
> >>>>  From three npt simulations of 72 ns with Berendsen barostat, I get
> the
> >>>> average volume is 298.5 nm^3.
> >>>>
> >>>> Continuing from a frame with volume very close to 298.5 nm^3 (~0.01
> >>>> deviation from this volume), I run NVT simulation that at first gives
> a
> >>>> system that doesn't seem to be at equilibrium.
> >>>>
> >>>>
> >> Does that time point correspond to the desired pressure?  The pressure
> >> tensor is calculated from the virial and the kinetic energy, so those
> are
> >> the quantities you should be looking at for instantaneous pressures.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==================================================
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