[gmx-users] How to adjust the box size to correct density?

[Chang Woon Jang]

Dear Abhishek Khetan,

  Thank you for your answer. It means that Gromacs does not automatically
adjust the box size even though NPT ensemble is employed. Am I right?

Different from Gromacs, Lammps automatically adjust box size when NPT
ensemble is applied during the simulation. Therefore, the density is able
to be fitted with initial conditions (pressure, temperature, simulation
time).

When I used the "gmx editconf" to resize the box to correct a density, vmd
shows a very ugly configurations. I think that topology file will check the
bond informations no matter how the gro file, containing only atom
coordinates and box size, looks like.

If I am wrong, please correct me.

Thank you.

Best regards,
Changwoon Jang

On Tue, Jan 5, 2016 at 1:16 PM, abhishek khetan <askhetan at gmail.com> wrote:

> To rescale the box.gro to a desired size using the actual density 543.21
> kg/l of the solvent and get a new scaled.gro file, I use this command:
>
> $ gmx editconf -f box.gro -density 543.21 -o scaled.gro > logfile
>
>
> On Tue, Jan 5, 2016 at 7:05 PM, Chang Woon Jang <changwoonjang at gmail.com>
> wrote:
>
> > Dear Gromacs Users,
> >
> >
> > I have a low density polymer system initially. I would like to fit the
> > correct liquid density using NPT simulation.
> >
> > I used Pcoupl=berendsen for 22 ns but the box size in confout.gro is
> still
> > the same as the input size of conf.gro.
> >
> > Initial in conf.gro (10.0 10.0 9.8)
> > output in confout.gro (10.0 10.0 9.8)
> >
> > My initial conditions are
> >
> > tau_p=5.0
> > compressibility=4.5e-5
> > ref_p=1.0
> >
> > Do I need to increase compressibility?
> >
> > Thank you.
> >
> >
> > Best regards,
> > Changwoon Jang,
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> abhishek
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