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

[Peter C. Lai]

Your starting topology is already broken if you have a non-integral total 
charge that's larger than the magnitude for floating point errors (in your
case, .000002 is floating point error, the 0.55 is systematic). Try figuring 
out where the charge assignments went wrong (the qtot column in the itp file 
is your friend).

On 2012-02-22 10:41:34AM +0300, James Starlight wrote:
> 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?
> 
> James
> 
> 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>
> >

> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 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


-- 
==================================================================
Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|
==================================================================