[gmx-users] Different number of molecules in simulation box.

[Mark Abraham]

Hi,

The number inserted depend on clashes with the input coordinates, so if you
change those, don't be surprised if the output changes :-)

Mark

On Wed, 3 May 2017 13:29 B Prakash <4gromacs at gmail.com> wrote:

> On Wed, May 3, 2017 at 3:53 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > On Wed, May 3, 2017 at 11:24 AM B Prakash <4gromacs at gmail.com> wrote:
> >
> > > Dear all,
> > > am trying to do a simulation of a protein in methanol. Am using gromacs
> > > 4.6.1.
> >
> >
> > Do yourself a favour and for new work, install a version that isn't four
> > years old, has extra bugs for free, and is unsupported ;-)
> >
>
> Dear Mark,
> thank you. I will do so. However, I was curious about the difference in the
> number of methanol molecules added when all other parameters are same.
>
> >
> > Am using the methanol box supplied in gromacs. In some of the
> > > simulations, the box took nearly 10K (10040) methanol molecules. But in
> > > others the number varied a little (10053). In editconf command, I tried
> > to
> > > center the protein in the simulation box. Is the variation in methanol
> > > molecules due to minor changes in orientation of protein by editconf
> and
> > > genbox. Please correct.
> > >
> >
> > Yes. There's an option to choose the maximum number of molecules added,
> if
> > you want a little more control.
> >
> > Mark
> >
> >
> > > Regards,
> > > Prakash.
> > > --
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