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

[Kathleen Kirchner]

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:

http://www.ime.unicamp.br/~martinez/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.

Best
Kathleen


-- 
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