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

[B Prakash]

Dear all,
am trying to do a simulation of a protein in methanol. Am using gromacs
4.6.1. 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.

Regards,
Prakash.