[gmx-users] -norandom option removed?

Justin Lemkul jalemkul at vt.edu
Wed Jan 15 17:48:14 CET 2014

On 1/15/14, 10:52 AM, Albert wrote:
> Hello:
> I found that the -norandom option in genion was no longer in 4.6.5:
> genion -h
> Option     Filename  Type         Description
> ------------------------------------------------------------
>    -s      topol.tpr  Input        Run input file: tpr tpb tpa
>    -n      index.ndx  Input, Opt.  Index file
>    -o        out.gro  Output       Structure file: gro g96 pdb etc.
>    -p      topol.top  In/Out, Opt. Topology file
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   yes     Print help info and quit
> -[no]version bool   no      Print version info and quit
> -nice        int    19      Set the nicelevel
> -np          int    0       Number of positive ions
> -pname       string NA      Name of the positive ion
> -pq          int    1       Charge of the positive ion
> -nn          int    0       Number of negative ions
> -nname       string CL      Name of the negative ion
> -nq          int    -1      Charge of the negative ion
> -rmin        real   0.6     Minimum distance between ions
> -seed        int    1993    Seed for random number generator
> -conc        real   0       Specify salt concentration (mol/liter). This will
>                              add sufficient ions to reach up to the specified
>                              concentration as computed from the volume of the
>                              cell in the input .tpr file. Overrides the -np
>                              and -nn options.
> -[no]neutral bool   no      This option will add enough ions to neutralize
>                              the system. These ions are added on top of those
>                              specified with -np/-nn or -conc.
> I am just wondering does it means the pme methods would be automatically for ion
> placement?

Non-random placement never really worked, so it was removed as an option.  Now, 
genion only places ions randomly.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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