[gmx-users] -norandom option removed?

Albert mailmd2011 at gmail.com
Wed Jan 15 17:00:36 CET 2014


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 
                             add sufficient ions to reach up to the 
                             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 
                             specified with -np/-nn or -conc.

I am just wondering does it means the pme methods would be automatically 
for ion placement?

thank you very much.

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