[gmx-users] High pressure

[Shreyas Kaptan]

>Why is the pressure not relieved in the Z-direction
That can only be answered predicated on the answer to the question if it
arises from the 0 compressibility. Also, what system are you using?

>Can I ignore it?

You should not. Your expected ensembles are in the 1 bar pressure regime.

On Thu, Jun 14, 2018 at 5:40 PM Alex <alexanderwien2k at gmail.com> wrote:

> Hi,
> The "compressibility          = 0.0 4.46e-5" means box is fixed in X-Y
> directions and free to change only in Z direction. I agree that fixing the
> box in two direction might be the reason for such huge pressure in spied
> of  setting the ref-p = 1. The question is that why the pressure does not
> ultimately get release in the Z direction?
> Also, is this pressure is an artificial pressure so that it can be ignored?
> If so, how I can find out (to be reported) the current real pressure in the
> system in such situation?
>
> Regards,
> Alex
>
> On Wed, Jun 13, 2018 at 5:30 PM, Shreyas Kaptan <shreyaskaptan at gmail.com>
> wrote:
>
> > That is indeed strange. Could it be because of the compressibility = 0 in
> > the first coordinate direction? if your simulations start with a badly
> > adjusted (minimized) structure in the TPR then it might get stuck there
> > because the 0 compressibility might not allow any change in the box
> > dimensions along that coordinate.
> >
> > Shreyas
> >
> > On Wed, Jun 13, 2018 at 7:47 PM Alex <alexanderwien2k at gmail.com> wrote:
> >
> > > Dear all,
> > > I have mixture of two types of short polymer in aqcuse solution on top
> > of a
> > > slab surface. After NVT equilibration, I run NPT with ref-p = 1
> > > semiisotropically, below is part of my npt.mdp file.
> > > I wonder why the pressure in the system is stable around *30000* after
> > 3ns
> > > in spite of of ref-p = 1?
> > >
> > >
> > > pcoupl                      = berendsen
> > > Pcoupltype               = semiisotropic
> > > tau-p                         = 2.0
> > > compressibility          = 0.0 4.46e-5
> > > ref-p                          = 1.0 1.0
> > > refcoord-scaling         = com
> > >
> > > Thanks.
> > > Regards,
> > > Alex
> > > --
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> > --
> > Shreyas Sanjay Kaptan
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-- 
Shreyas Sanjay Kaptan