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

James Starlight jmsstarlight at gmail.com
Wed Feb 22 08:41:34 CET 2012

Dear all :)

I have one extra question about Genion.

I want to neitralise my system with the qtot - 1.550002e by placing some Na
and Cl ions under the physiological concetrantion 100 mmol/l

I've performed

genion -s ions.tpr -o b2ar_ions.gro -p topol.top -pname NA -nname CL -conc
0.1 -neutral

but insytead I've obtained system with 4.499977e-01 changre

What should I do to fix this problem?


2012/2/16 Kathleen Kirchner <kirchner at mis.mpg.de>

> 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/<http://www.ime.unicamp.br/%7Emartinez/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/<http://www.mis.mpg.de/scicomp/CompPhysChem/>
> Tel +49 341 9959 725
> Fax +49 341 9959 999
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120222/a1218a84/attachment.html>

More information about the gromacs.org_gmx-users mailing list