[gmx-users] High pressure
alexanderwien2k at gmail.com
Thu Jun 14 17:40:42 CEST 2018
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?
On Wed, Jun 13, 2018 at 5:30 PM, Shreyas Kaptan <shreyaskaptan at gmail.com>
> 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.
> 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
> > 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
> > --
> > Gromacs Users mailing list
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> Shreyas Sanjay Kaptan
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users