[gmx-users] editconf -density

[Mark Abraham]

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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