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

[B Prakash]

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.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>