[gmx-users] Re: Placing ions in the specified positions

Kathleen Kirchner kirchner at mis.mpg.de
Thu Feb 16 12:54:47 CET 2012

Dear James,

I was working for a longer time on ion placement within more or less 
equilibrated structures. I found my nearly magical miracle solving those 
problems in not using any gromacs tool for producing the input structure 
but rather use the free software Packmol:


The software solves a mathematical minimization problem instead of 
putting somewhere molecules and deleting others.

After a short energy minimization of the obtained output structure (a 
few 100 steps of steep algorithm) usally my systems work fine.


Kathleen Kirchner
PhD student
Max Planck Institute for Mathematics in the Sciences
(MPI f. Mathematik in den Naturwissenschaften)
Inselstr. 22-26, D04103 Leipzig
e-mail: kirchner at mis.mpg.de
web: http://www.mis.mpg.de/scicomp/CompPhysChem/
Tel +49 341 9959 725
Fax +49 341 9959 999

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