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GMX-GENRESTR(1)			    GROMACS		       GMX-GENRESTR(1)

NAME
       gmx-genrestr  - Generate	position restraints or distance	restraints for
       index groups

SYNOPSIS
	  gmx genrestr [-f [_.gro/.g96/..._]] [-n [_.ndx_]] [-o	[_.itp_]]
		       [-of [_.ndx_]] [-fc _vector_] [-freeze _real_]
		       [-[no]disre] [-disre_dist _real_] [-disre_frac _real_]
		       [-disre_up2 _real_] [-cutoff _real_] [-[no]constr]

DESCRIPTION
       gmx genrestr produces an	#include file for a topology containing	a list
       of  atom	numbers	and three force	constants for the x-, y-, and z-direc-
       tion based on the contents of the -f file.  A  single  isotropic	 force
       constant	may be given on	the command line instead of three components.

       WARNING:	 Position restraints are interactions within molecules,	there-
       fore they must be included within the correct [ moleculetype ] block in
       the topology. The atom indices within the [ position_restraints ] block
       must be within the range	of the atom indices for	 that  molecule	 type.
       Since the atom numbers in every moleculetype in the topology start at 1
       and the numbers in the input file for gmx genrestr number consecutively
       from 1, gmx genrestr will only produce a	useful file for	the first mol-
       ecule. You may wish to edit the resulting  index	 file  to  remove  the
       lines  for  later atoms,	or construct a suitable	index group to provide
       as input	to gmx genrestr.

       The -of option produces an index	file that can  be  used	 for  freezing
       atoms. In this case, the	input file must	be a .pdb file.

       With  the -disre	option,	half a matrix of distance restraints is	gener-
       ated instead of position	restraints. With this matrix, that  one	 typi-
       cally  would  apply  to Calpha atoms in a protein, one can maintain the
       overall conformation of a protein without tieing	it to a	specific posi-
       tion (as	with position restraints).

OPTIONS
       Options to specify input	files:

       -f [<.gro/.g96/^a|>] (conf.gro)
	      Structure	file: gro g96 pdb brk ent esp tpr

       -n [<.ndx>] (index.ndx) (Optional)
	      Index file

       Options to specify output files:

       -o [<.itp>] (posre.itp)
	      Include file for topology

       -of [<.ndx>] (freeze.ndx) (Optional)
	      Index file

       Other options:

       -fc <vector> (1000 1000 1000)
	      Force constants (kJ/mol nm^2)

       -freeze <real> (0)
	      If  the  -of  option  or this one	is given an index file will be
	      written containing atom numbers of all atoms that	have a	B-fac-
	      tor less than the	level given here

       -[no]disre (no)
	      Generate a distance restraint matrix for all the atoms in	index

       -disre_dist <real> (0.1)
	      Distance	range  around  the actual distance for generating dis-
	      tance restraints

       -disre_frac <real> (0)
	      Fraction of distance to be used as interval rather than a	 fixed
	      distance.	 If the	fraction of the	distance that you specify here
	      is less than the distance	given in the previous option, that one
	      is used instead.

       -disre_up2 <real> (1)
	      Distance	between	 upper	bound for distance restraints, and the
	      distance at which	the force becomes constant (see	manual)

       -cutoff <real> (-1)
	      Only generate distance restraints	for atoms pairs	within	cutoff
	      (nm)

       -[no]constr (no)
	      Generate	a  constraint  matrix rather than distance restraints.
	      Constraints of type 2 will be generated that do generate	exclu-
	      sions.

SEE ALSO
       gmx(1)

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

COPYRIGHT
       2020, GROMACS development team

2020.4				 Oct 06, 2020		       GMX-GENRESTR(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT

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