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gmx-genion(1)			GROMACS	Manual			 gmx-genion(1)

NAME
       gmx-genion  - Generate monoatomic ions on energetically favorable posi-
       tions

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

DESCRIPTION
       gmx genion randomly replaces solvent molecules  with  monoatomic	 ions.
       The  group  of solvent molecules	should be continuous and all molecules
       should have the same number of atoms. The user should add the ion mole-
       cules to	the topology file or use the -p	option to automatically	modify
       the topology.

       The ion molecule	type, residue and atom names in	all force  fields  are
       the  capitalized	 element names without sign. This molecule name	should
       be given	with -pname or -nname, and the	[molecules]  section  of  your
       topology	 updated accordingly, either by	hand or	with -p. Do not	use an
       atom name instead!

       Ions which can have multiple charge states get the multiplicity	added,
       without sign, for the uncommon states only.

       For  larger  ions,  e.g.	sulfate	we recommended using gmx insert\-mole-
       cules.

OPTIONS
       Options to specify input	and output files:

       -s [_.tpr/.tpb/..._] (topol.tpr)	(Input)
	   Run input file: tpr tpb tpa

       -n [_.ndx_] (index.ndx) (Input, Optional)
	   Index file

       -o [_.gro/.g96/..._] (out.gro) (Output)
	   Structure file: gro g96 pdb brk ent esp

       -p [_.top_] (topol.top) (Input/Output, Optional)
	   Topology file

       Other options:

       -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  (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.

KNOWN ISSUES
       - If you	specify	a salt concentration existing ions are not taken  into
       account.	 In  effect  you  therefore  specify  the amount of salt to be
       added.

SEE ALSO
       gromacs(7)

       More  information  about	 GROMACS  is  available	 at   <http://www.gro-
       macs.org/>.

VERSION	5.0.6							 gmx-genion(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | KNOWN ISSUES | SEE ALSO

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