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

Mark Abraham mark.j.abraham at gmail.com
Wed May 3 12:23:46 CEST 2017


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 ;-)

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.


> Regards,
> Prakash.
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