1genion(1) GROMACS suite, VERSION 4.5 genion(1)
2
6 genion - generates mono atomic ions on energetically favorable posi‐
7 tions
8 VERSION 4.5
10
12 genion -s topol.tpr -table table.xvg -n index.ndx -o out.gro -g
13 genion.log -pot pot.pdb -p topol.top -[no]h -[no]version -nice int -xvg
14 enum -np int -pname string -pq int -nn int -nname string -nq int -rmin
15 real -[no]random -seed int -scale real -conc real -[no]neutral
16
18 genion replaces solvent molecules by monoatomic ions at the position of
19 the first atoms with the most favorable electrostatic potential or at
20 random. The potential is calculated on all atoms, using normal GROMACS
21 particle based methods (in contrast to other methods based on solving
22 the Poisson-Boltzmann equation). The potential is recalculated after
23 every ion insertion. If specified in the run input file, a reaction
24 field, shift function or user function can be used. For the user func‐
25 tion a table file can be specified with the option -table. The group
26 of solvent molecules should be continuous and all molecules should have
27 the same number of atoms. The user should add the ion molecules to the
28 topology file or use the -p option to automatically modify the topol‐
29 ogy.
30 The ion molecule type, residue and atom names in all force fields are
33 the capitalized element names without sign. Ions which can have multi‐
34 ple charge states get the multiplicilty added, without sign, for the
35 uncommon states only.
36 With the option -pot the potential can be written as B-factors in a
39 pdb file (for visualisation using e.g. rasmol). The unit of the poten‐
40 tial is 1000 kJ/(mol e), the scaling be changed with the -scale
41 option.
42 For larger ions, e.g. sulfate we recommended to use genbox.
45
47 -s topol.tpr Input
48 Run input file: tpr tpb tpa
49 -table table.xvg Input, Opt.
51 xvgr/xmgr file
52 -n index.ndx Input, Opt.
54 Index file
55 -o out.gro Output
57 Structure file: gro g96 pdb etc.
58 -g genion.log Output
60 Log file
61 -pot pot.pdb Output, Opt.
63 Protein data bank file
64 -p topol.top In/Out, Opt.
66 Topology file
67
70 -[no]hno
71 Print help info and quit
72 -[no]versionno
74 Print version info and quit
75 -nice int 19
77 Set the nicelevel
78 -xvg enum xmgrace
80 xvg plot formatting: xmgrace, xmgr or none
81 -np int 0
83 Number of positive ions
84 -pname string NA
86 Name of the positive ion
87 -pq int 1
89 Charge of the positive ion
90 -nn int 0
92 Number of negative ions
93 -nname string CL
95 Name of the negative ion
96 -nq int -1
98 Charge of the negative ion
99 -rmin real 0.6
101 Minimum distance between ions
102 -[no]randomyes
104 Use random placement of ions instead of based on potential. The rmin
105 option should still work
106 -seed int 1993
108 Seed for random number generator
109 -scale real 0.001
111 Scaling factor for the potential for -pot
112 -conc real 0
114 Specify salt concentration (mol/liter). This will add sufficient ions
115 to reach up to the specified concentration as computed from the volume
116 of the cell in the input tpr file. Overrides the -np and nn options.
117 -[no]neutralno
119 This option will add enough ions to neutralize the system. In combina‐
120 tion with the concentration option a neutral system at a given salt
121 concentration will be generated.
122
125 - Calculation of the potential is not reliable, therefore the -random
126 option is now turned on by default.
127 - If you specify a salt concentration existing ions are not taken into
129 account. In effect you therefore specify the amount of salt to be
130 added.
131
134 gromacs(7)
135 More information about GROMACS is available at <http://www.gro‐
137 macs.org/>.
138 Thu 26 Aug 2010 genion(1)