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

[B Prakash]

On Wed, May 3, 2017 at 5:22 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

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

Hi Mark,
surprisingly, there were no changes in neither the pdb file nor the input
commands. However genbox accomodated 13 more methanol molecules in the same
space. The only reason for it I could imagine is minor changes in protein
orientation.

>
> 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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