[gmx-users] Pressure coupling with stochastic integrator for triclinic box
haiyang.logan.zhang at gmail.com
Tue Aug 26 10:57:01 CEST 2014
On Tue, Aug 26, 2014 at 4:34 PM, Mark Abraham <mark.j.abraham at gmail.com>
> It's hard to help without actual details of your P-R settings and GROMACS
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.
> 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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