genrestr(1) [debian man page]
genrestr(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c genrestr(1) NAME
genrestr - generates position restraints or distance restraints for index groups VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
genrestr -f conf.gro -n index.ndx -o posre.itp -of freeze.ndx -[no]h -[no]version -nice int -fc vector -freeze real -[no]disre -disre_dist real -disre_frac real -disre_up2 real -cutoff real -[no]constr DESCRIPTION
genrestr produces an include file for a topology containing a list of atom numbers and three force constants for the x-, y-, and z-direction. A single isotropic force constant may be given on the command line instead of three components. WARNING: position restraints only work for the one molecule at a time. Position restraints are interactions within molecules, therefore they should be included within the correct [ moleculetype ] block in the topology. Since the atom numbers in every moleculetype in the topology start at 1 and the numbers in the input file for genrestr number consecutively from 1, genrestr will only produce a useful file for the first molecule. 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 generated 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 position (as with position restraints). FILES
-f conf.gro Input Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt. Index file -o posre.itp Output Include file for topology -of freeze.ndx Output, Opt. Index file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 0 Set the nicelevel -fc vector 1000 1000 1000 force constants (kJ/mol nm2) -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-factor less than the level given here -[no]disreno Generate a distance restraint matrix for all the atoms in index -disre_dist real 0.1 Distance range around the actual distance for generating distance 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]constrno Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions. SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 genrestr(1)
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g_mindist(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_mindist(1) NAME
g_mindist - calculates the minimum distance between two groups VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_mindist -f traj.xtc -s topol.tpr -n index.ndx -od mindist.xvg -on numcont.xvg -o atm-pair.out -ox mindist.xtc -or mindistres.xvg -[no]h -[no]version -nice int -b time -e time -dt time -tu enum -[no]w -xvg enum -[no]matrix -[no]max -d real -[no]group -[no]pi -[no]split -ng int -[no]pbc -[no]respertime -[no]printresname DESCRIPTION
g_mindist computes the distance between one group and a number of other groups. Both the minimum distance (between any pair of atoms from the respective groups) and the number of contacts within a given distance are written to two separate output files. With the -group option a contact of an atom in other group with multiple atoms in the first group is counted as one contact instead of as multiple con- tacts. With -or, minimum distances to each residue in the first group are determined and plotted as a function of residue number. With option -pi the minimum distance of a group to its periodic image is plotted. This is useful for checking if a protein has seen its periodic image during a simulation. Only one shift in each direction is considered, giving a total of 26 shifts. It also plots the maximum distance within the group and the lengths of the three box vectors. Other programs that calculate distances are g_dist and g_bond. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -od mindist.xvg Output xvgr/xmgr file -on numcont.xvg Output, Opt. xvgr/xmgr file -o atm-pair.out Output, Opt. Generic output file -ox mindist.xtc Output, Opt. Trajectory: xtc trr trj gro g96 pdb -or mindistres.xvg Output, Opt. xvgr/xmgr file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: fs, ps, ns, us, ms or s -[no]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]matrixno Calculate half a matrix of group-group distances -[no]maxno Calculate *maximum* distance instead of minimum -d real 0.6 Distance for contacts -[no]groupno Count contacts with multiple atoms in the first group as one -[no]pino Calculate minimum distance with periodic images -[no]splitno Split graph where time is zero -ng int 1 Number of secondary groups to compute distance to a central group -[no]pbcyes Take periodic boundary conditions into account -[no]respertimeno When writing per-residue distances, write distance for each time point -[no]printresnameno Write residue names SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_mindist(1)