[gmx-users] Re: How to can i replace a molecule

Dr. Vitaly Chaban vvchaban at gmail.com
Sun Oct 7 14:18:53 CEST 2012

> Dear All users
> How to can i replace a molecule(for example methane) with another
> molecule(propane)?
> Number of these molecules are given and their position is random,
> Can I use genbox or genion, How to do i do it?

Since propane is significantly larger than methane, it is impossible
without blowing up your system.

I would remove methanes by hand and then insert propanes using any
utility you like, but you will need to increase your box to provide
more space.

Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark

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