1GMX-GENION(1)                       GROMACS                      GMX-GENION(1)
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NAME

6       gmx-genion  - Generate monoatomic ions on energetically favorable posi‐
7       tions
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SYNOPSIS

10          gmx genion [-s [<.tpr>]] [-n [<.ndx>]] [-p [<.top>]]
11                     [-o [<.gro/.g96/...>]] [-np <int>] [-pname <string>]
12                     [-pq <int>] [-nn <int>] [-nname <string>] [-nq <int>]
13                     [-rmin <real>] [-seed <int>] [-conc <real>] [-[no]neutral]
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DESCRIPTION

16       gmx genion randomly replaces solvent molecules  with  monoatomic  ions.
17       The  group  of solvent molecules should be continuous and all molecules
18       should have the same number of atoms.  The user should add the ion mol‐
19       ecules  to the topology file or use the -p option to automatically mod‐
20       ify the topology.
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22       The ion molecule type, residue and atom names in all force  fields  are
23       the  capitalized  element names without sign. This molecule name should
24       be given with -pname or -nname, and the  [molecules]  section  of  your
25       topology  updated accordingly, either by hand or with -p. Do not use an
26       atom name instead!
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28       Ions which can have multiple charge states get the multiplicity  added,
29       without sign, for the uncommon states only.
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31       For  larger  ions,  e.g.  sulfate we recommended using gmx insert-mole‐
32       cules.
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OPTIONS

35       Options to specify input files:
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37       -s [<.tpr>] (topol.tpr)
38              Portable xdr run input file
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40       -n [<.ndx>] (index.ndx) (Optional)
41              Index file
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43       Options to specify input/output files:
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45       -p [<.top>] (topol.top) (Optional)
46              Topology file
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48       Options to specify output files:
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50       -o [<.gro/.g96/…>] (out.gro)
51              Structure file: gro g96 pdb brk ent esp
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53       Other options:
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55       -np <int> (0)
56              Number of positive ions
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58       -pname <string> (NA)
59              Name of the positive ion
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61       -pq <int> (1)
62              Charge of the positive ion
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64       -nn <int> (0)
65              Number of negative ions
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67       -nname <string> (CL)
68              Name of the negative ion
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70       -nq <int> (-1)
71              Charge of the negative ion
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73       -rmin <real> (0.6)
74              Minimum distance between ions
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76       -seed <int> (0)
77              Seed for random number generator (0 means generate)
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79       -conc <real> (0)
80              Specify salt concentration (mol/liter). This will add sufficient
81              ions to reach up to the specified concentration as computed from
82              the volume of the cell in the input .tpr file. Overrides the -np
83              and -nn options.
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85       -[no]neutral (no)
86              This option will add enough ions to neutralize the system. These
87              ions are added on top of those specified with -np/-nn or -conc.
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KNOWN ISSUES

90       · If you specify a salt concentration existing ions are not taken  into
91         account.  In  effect  you  therefore specify the amount of salt to be
92         added.
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SEE ALSO

95       gmx(1)
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97       More    information    about    GROMACS    is    available    at     <‐
98       http://www.gromacs.org/>.
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101       2019, GROMACS development team
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1062019.2                           Apr 16, 2019                    GMX-GENION(1)
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