[gmx-users] High pressure

[Alex]

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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