[gmx-users] editconf -density

[James Lord]

Thanks Dan and Mark,
Mark approach gave me I what I wanted.


On Mon, Aug 10, 2015 at 4:43 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> That is unlikely to work for large changes in density, because bond lengths
> get messed up too badly. Instead, you can use Berendsen pressure coupling
> with a larger or smaller target pressure to slowly change the volume in an
> actual simulation. Equilibrate thoroughly afterwards!
>
> Mark
>
> On Sun, 9 Aug 2015 18:27 Dan Sponseller <gromacs at danpeg.com> wrote:
>
> > You do not state your original density. But lets say you need to reduce
> > volume 3% to get your correct density. Use:
> > ediftconf -f solv_large.gro -o solv_large_scaled.gro -scale 1 1 0.97
> >
> > Just do a quick side calculation for what you need and substitute in for
> > 0.97.
> >
> > Dan
> >
> >
> > > On Aug 9, 2015, at 4:18 AM, James Lord <jjamesgreen110 at gmail.com>
> wrote:
> > >
> > > Hi all,
> > > I have  a solvent filled in a box of dimensions 12 12 12
> > (solv_large.gro).
> > > I want to adjust the density of system to 824 kg/m3. But I want
> editconf
> > to
> > > just change the volume only by changing the z direction ? is that
> > possible?
> > > I did
> > > ediftconf -f solv_large.gro -o solv_large_scaled.gro -density 824
> > >
> > > But it changes the x,y,z to adjust the density. Is it possible to ask
> > > editconf to do this only by changing for example z?
> > > Cheers
> > > James
> > > --
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