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: [email protected]
web: http://www.mis.mpg.de/scicomp/CompPhysChem/
Tel +49 341 9959 725
Fax +49 341 9959 999
--
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