[gmx-users] Pressure coupling with stochastic integrator for triclinic box

[Mark Abraham]

Hi,

1) GROMACS 4.5.5 is pretty old, so we aren't going to spend time trouble
shooting things that might have been fixed since then. Please try out
GROMACS 5, where there is a brand new SD integrator, and faster performance
all round.

2) 80 +/- 3000 is not terribly significant. What gives you greater
confidence about your Berendsen result? It seems like you need either a
larger system or a lot more sampling. See also
http://www.gromacs.org/Documentation/Terminology/Pressure

Mark




On Tue, Aug 26, 2014 at 10:56 AM, Haiyang Zhang <
haiyang.logan.zhang at gmail.com> wrote:

> On Tue, Aug 26, 2014 at 4:34 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > It's hard to help without actual details of your P-R settings and GROMACS
> > version!
>
> Pcoupl                     = Parrinello-rahman
> Pcoupltype               = anisotropic
> tau_p                       = 15
> compressibility          = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 0 0
> ref_p                         = 1 1 1 1 0 0
>
> GROMACS version: 4.5.5
>
> Do things work with non-stochastic integrators?
> >
> For anisotropic, I have turned on/off off-diagonal pressure components. The
> best setting is listed above. Using this setup with a normal md integrator,
> I got a pressure of -1 +/- 2716 bar, which seems OK.
>
> However, for SD integrator, P is 80 +/- 3405 bar. When turning off all
> off-diagonal components, P is 13 +/- 3520 bar. If using isotropic PR with
> SD, P is 15 +/- 3516. All the simulations were done for 5 ns.
>
> Thank you very much.
>
> >
> > Mark
> >
> >
> > On Tue, Aug 26, 2014 at 10:00 AM, Haiyang Zhang <
> > haiyang.logan.zhang at gmail.com> wrote:
> >
> > > Dear Gmx Users,
> > >
> > > Recently, I used Parrinello-rahman (PR) pressure coupling to simulate a
> > > periodic metal-organic framework (MOF) system. The box is triclinic
> with
> > > angles of 90, 90, 120 degree.The system was simulated using a
> stochastic
> > > integrator. Isotropic and anisotropic pressure coupling have been
> tested,
> > > and the results show that PR method does not give correct pressures.
> > >
> > > However, a more robust berendsen (BD) method can give the reasonable
> > > pressures for both isotropic and anisotropic coupling. PR is known to
> > > perform better than BD, so I prefer to use PR to couple poressure.
> > >
> > > Did someone have any clue fixing this problem ? Thanks in advance.
> > >
> > > With my best wishes, Haiyang
> > > --
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