Added a few files to fix the build system.

A few man pages were missing, and I did some cleanup in
programs.txt so that it's not quite such a mashup of randomly
listed programs.

diff --git a/admin/programs.txt b/admin/programs.txt
index affb01d72bbaad6650a819f8ba83b291ef4032ac..049c549581887bd69961973938ea07b09ca52937 100644 (file)
--- a/admin/programs.txt
+++ b/admin/programs.txt
@@ -1,164 +1,164 @@
 HEAD|Generating topologies and coordinates
-pdb2gmx|converts pdb files to topology and coordinate files
-g_x2top|generates a primitive topology from coordinates 
 editconf|edits the box and writes subgroups 
+g_protonate|protonates structures
+g_x2top|generates a primitive topology from coordinates 
 genbox|solvates a system
-genion|generates mono atomic ions on energetically favorable positions
 genconf|multiplies a conformation in 'random' orientations
+genion|generates mono atomic ions on energetically favorable positions
 genrestr|generates position restraints or distance restraints for index groups
-g_protonate|protonates structures
+pdb2gmx|converts coordinate files to topology and FF-compliant coordinate files
 END
 
 HEAD|Running a simulation
 grompp|makes a run input file
-tpbconv|makes a run input file for restarting a crashed run
 mdrun|performs a simulation, do a normal mode analysis or an energy minimization
+tpbconv|makes a run input file for restarting a crashed run
 END
 
 HEAD|Viewing trajectories
-ngmx|displays a trajectory
 g_nmtraj|generate a virtual trajectory from an eigenvector
+ngmx|displays a trajectory
 END
 
 HEAD|Processing energies
-g_energy|writes energies to xvg files and displays averages
 g_enemat|extracts an energy matrix from an energy file
+g_energy|writes energies to xvg files and displays averages
 mdrun|with -rerun (re)calculates energies for trajectory frames
 END
 
 HEAD|Converting files
 editconf|converts and manipulates structure files
-trjconv|converts and manipulates trajectory files
-trjcat|concatenates trajectory files
 eneconv|converts energy files
-xpm2ps|converts XPM matrices to encapsulated postscript (or XPM)
 g_sigeps|convert c6/12 or c6/cn combinations to and from sigma/epsilon
+trjcat|concatenates trajectory files
+trjconv|converts and manipulates trajectory files
+xpm2ps|converts XPM matrices to encapsulated postscript (or XPM)
 END
 
 HEAD|Tools
-make_ndx|makes index files
-mk_angndx|generates index files for g_angle
-gmxcheck|checks and compares files
-gmxdump|makes binary files human readable
-g_traj|plots x, v and f of selected atoms/groups (and more) from a trajectory
 g_analyze|analyzes data sets
-trjorder|orders molecules according to their distance to a group
+g_dyndom|interpolate and extrapolate structure rotations
 g_filter|frequency filters trajectories, useful for making smooth movies
 g_lie|free energy estimate from linear combinations
-g_dyndom|interpolate and extrapolate structure rotations
 g_morph|linear interpolation of conformations 
-g_wham|weighted histogram analysis after umbrella sampling
-xpm2ps|convert XPM (XPixelMap) file to postscript
+g_pme_error|estimates the error of using PME with a given input file
+g_select|selects groups of atoms based on flexible textual selections
 g_sham|read/write xmgr and xvgr data sets
 g_spatial|calculates the spatial distribution function
-g_select|selects groups of atoms based on flexible textual selections
-g_pme_error|estimates the error of using PME with a given input file
+g_traj|plots x, v and f of selected atoms/groups (and more) from a trajectory
 g_tune_pme|time mdrun as a function of PME nodes to optimize settings
+g_wham|weighted histogram analysis after umbrella sampling
+gmxcheck|checks and compares files
+gmxdump|makes binary files human readable
+make_ndx|makes index files
+mk_angndx|generates index files for g_angle
+trjorder|orders molecules according to their distance to a group
+xpm2ps|convert XPM (XPixelMap) file to postscript
 END
 
 HEAD|Distances between structures
-g_rms|calculates rmsd's with a reference structure and rmsd matrices
-g_confrms|fits two structures and calculates the rmsd 
 g_cluster|clusters structures
+g_confrms|fits two structures and calculates the rmsd 
+g_rms|calculates rmsd's with a reference structure and rmsd matrices
 g_rmsf|calculates atomic fluctuations
 END
 
 HEAD|Distances in structures over time
-g_mindist|calculates the minimum distance between two groups
-g_dist|calculates the distances between the centers of mass of two groups
 g_bond|calculates distances between atoms
+g_dist|calculates the distances between the centers of mass of two groups
+g_mindist|calculates the minimum distance between two groups
 g_mdmat|calculates residue contact maps
 g_polystat|calculates static properties of polymers
 g_rmsdist|calculates atom pair distances averaged with power -2, -3 or -6
 END
 
 HEAD|Mass distribution properties over time
-g_traj|plots x, v, f, box, temperature and rotational energy
 g_gyrate|calculates the radius of gyration
 g_msd|calculates mean square displacements
 g_polystat|calculates static properties of polymers
-g_rotacf|calculates the rotational correlation function for molecules
 g_rdf|calculates radial distribution functions
+g_rotacf|calculates the rotational correlation function for molecules
 g_rotmat|plots the rotation matrix for fitting to a reference structure
+g_traj|plots x, v, f, box, temperature and rotational energy
 g_vanhove|calculates Van Hove displacement functions
 END
 
 HEAD|Analyzing bonded interactions
-g_bond|calculates bond length distributions
-mk_angndx|generates index files for g_angle
 g_angle|calculates distributions and correlations for angles and dihedrals
+g_bond|calculates bond length distributions
 g_dih|analyzes dihedral transitions
+mk_angndx|generates index files for g_angle
 END
 
 HEAD|Structural properties
+g_anadock|cluster structures from Autodock runs
+g_bundle|analyzes bundles of axes, e.g. helices
+g_clustsize|calculate size distributions of atomic clusters
+g_disre|analyzes distance restraints
 g_hbond|computes and analyzes hydrogen bonds
-g_saltbr|computes salt bridges
-g_sas|computes solvent accessible surface area
 g_order|computes the order parameter per atom for carbon tails
 g_principal|calculates axes of inertia for a group of atoms
 g_rdf|calculates radial distribution functions
+g_saltbr|computes salt bridges
+g_sas|computes solvent accessible surface area
 g_sgangle|computes the angle and distance between two groups
 g_sorient|analyzes solvent orientation around solutes
 g_spol|analyzes solvent dipole orientation and polarization around solutes
-g_bundle|analyzes bundles of axes, e.g. helices
-g_disre|analyzes distance restraints
-g_clustsize|calculate size distributions of atomic clusters
-g_anadock|cluster structures from Autodock runs
 END
 
 HEAD|Kinetic properties
-g_traj|plots x, v, f, box, temperature and rotational energy
-g_velacc|calculates velocity autocorrelation functions
-g_tcaf|calculates viscosities of liquids
 g_bar|calculates free energy difference estimates through Bennett's acceptance ratio
 g_current|calculate current autocorrelation function of system
-g_vanhove|compute Van Hove correlation function
 g_principal|calculate principal axes of inertion for a group of atoms
+g_tcaf|calculates viscosities of liquids
+g_traj|plots x, v, f, box, temperature and rotational energy
+g_vanhove|compute Van Hove correlation function
+g_velacc|calculates velocity autocorrelation functions
 END
 
 HEAD|Electrostatic properties
-genion|generates mono atomic ions on energetically favorable positions
-g_potential|calculates the electrostatic potential across the box
-g_dipoles|computes the total dipole plus fluctuations
-g_dielectric|calculates frequency dependent dielectric constants
 g_current|calculates dielectric constants for charged systems
+g_dielectric|calculates frequency dependent dielectric constants
+g_dipoles|computes the total dipole plus fluctuations
+g_potential|calculates the electrostatic potential across the box
 g_spol|analyze dipoles around a solute
+genion|generates mono atomic ions on energetically favorable positions
 END
 
-HEAD|Protein specific analysis
+HEAD|Protein-specific analysis
 do_dssp|assigns secondary structure and calculates solvent accessible surface area
 g_chi|calculates everything you want to know about chi and other dihedrals
 g_helix|calculates basic properties of alpha helices
 g_helixorient|calculates local pitch/bending/rotation/orientation inside helices
 g_rama|computes Ramachandran plots
-g_xrama|shows animated Ramachandran plots
 g_wheel|plots helical wheels
+g_xrama|shows animated Ramachandran plots
 END
 
 HEAD|Interfaces
-g_potential|calculates the electrostatic potential across the box
+g_bundle|analyzes bundles of axes, e.g. transmembrane helices
 g_density|calculates the density of the system
 g_densmap|calculates 2D planar or axial-radial density maps
 g_densorder|calculate surface fluctuations
-g_order|computes the order parameter per atom for carbon tails
 g_h2order|computes the orientation of water molecules
-g_bundle|analyzes bundles of axes, e.g. transmembrane helices
+g_hydorder|computes tetrahedrality parameters around a given atom
+g_order|computes the order parameter per atom for carbon tails
 g_membed|embeds a protein into a lipid bilayer
+g_potential|calculates the electrostatic potential across the box
 END
 
 
 HEAD|Covariance analysis
-g_covar|calculates and diagonalizes the covariance matrix
 g_anaeig|analyzes the eigenvectors
+g_covar|calculates and diagonalizes the covariance matrix
 make_edi|generate input files for essential dynamics sampling
 END
 
 HEAD|Normal modes
-grompp|makes a run input file
-mdrun|finds a potential energy minimum
-mdrun|calculates the Hessian
+g_anaeig|analyzes the normal modes
 g_nmeig|diagonalizes the Hessian 
 g_nmtraj|generate oscillating trajectory of an eigenmode
-g_anaeig|analyzes the normal modes
 g_nmens|generates an ensemble of structures from the normal modes
+grompp|makes a run input file
+mdrun|finds a potential energy minimum and calculates the Hessian
 END

diff --git a/man/man1/g_options.1 b/man/man1/g_options.1
new file mode 100644 (file)
index 0000000..5c0a41c
--- /dev/null
+++ b/man/man1/g_options.1
@@ -0,0 +1,49 @@
+.TH g_options 1 "Sun 10 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110410-e5eb052-dirty"
+.SH NAME
+g_options
+.B VERSION 4.5.4-dev-20110410-e5eb052-dirty
+.SH SYNOPSIS
+\f3g_options\fP
+.BI "\-[no]h" ""
+.BI "\-[no]version" ""
+.BI "\-nice" " int "
+.SH DESCRIPTION
+\&GROMACS programs have some standard options,
+\&of which some are hidden by default:
+.SH OTHER OPTIONS
+.BI "\-[no]h"  "no    "
+ Print help info and quit
+
+.BI "\-[no]version"  "no    "
+ Print version info and quit
+
+.BI "\-nice"  " int" " 0" 
+ Set the nicelevel
+
+.SH KNOWN PROBLEMS
+\- If the configuration script found Motif or Lesstif on your system, you can use the graphical interface (if not, you will get an error):
+\fB \-X\fR gmx_bool \fB no\fR Use dialog box GUI to edit command line options
+
+\- When compiled on an SGI\-IRIX system, all GROMACS programs have an additional option:
+\fB \-npri\fR int \fB 0\fR Set non blocking priority (try 128)
+
+\- Optional files are not used unless the option is set, in contrast to non\-optional files, where the default file name is used when the option is not set.
+
+\- All GROMACS programs will accept file options without a file extension or filename being specified. In such cases the default filenames will be used. With multiple input file types, such as generic structure format, the directory will be searched for files of each type with the supplied or default name. When no such file is found, or with output files the first file type will be used.
+
+\- All GROMACS programs with the exception of \fB mdrun\fR and \fB eneconv\fR check if the command line options are valid.  If this is not the case, the program will be halted.
+
+\- Enumerated options (enum) should be used with one of the arguments listed in the option description, the argument may be abbreviated. The first match to the shortest argument in the list will be selected.
+
+\- Vector options can be used with 1 or 3 parameters. When only one parameter is supplied the two others are also set to this value.
+
+\- All GROMACS programs can read compressed or g\-zipped files. There might be a problem with reading compressed \fB .xtc\fR, \fB .trr\fR and \fB .trj\fR files, but these will not compress very well anyway.
+
+\- Most GROMACS programs can process a trajectory with fewer atoms than the run input or structure file, but only if the trajectory consists of the first n atoms of the run input or structure file.
+
+\- Many GROMACS programs will accept the \fB \-tu\fR option to set the time units to use in output files (e.g. for \fB xmgr\fR graphs or \fB xpm\fR matrices) and in all time options.
+
+.SH SEE ALSO
+.BR gromacs(7)
+
+More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.

diff --git a/man/man1/g_pme_error.1 b/man/man1/g_pme_error.1
new file mode 100644 (file)
index 0000000..a3c313e
--- /dev/null
+++ b/man/man1/g_pme_error.1
@@ -0,0 +1,70 @@
+.TH g_pme_error 1 "Sun 10 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110410-e5eb052-dirty"
+.SH NAME
+g_pme_error - estimates the error of using PME with a given input file
+
+.B VERSION 4.5.4-dev-20110410-e5eb052-dirty
+.SH SYNOPSIS
+\f3g_pme_error\fP
+.BI "\-s" " topol.tpr "
+.BI "\-o" " error.out "
+.BI "\-so" " tuned.tpr "
+.BI "\-[no]h" ""
+.BI "\-[no]version" ""
+.BI "\-nice" " int "
+.BI "\-beta" " real "
+.BI "\-[no]tune" ""
+.BI "\-self" " real "
+.BI "\-seed" " int "
+.BI "\-[no]v" ""
+.SH DESCRIPTION
+\&\fB g_pme_error\fR estimates the error of the electrostatic forces
+\&if using the sPME algorithm. The flag \fB \-tune\fR will determine
+\&the splitting parameter such that the error is equally
+\&distributed over the real and reciprocal space part.
+\&The part of the error that stems from self interaction of the particles is computationally demanding. However, a good a approximation is to
+\&just use a fraction of the particles for this term which can be
+\&indicated by the flag \fB \-self\fR.
+
+
+.SH FILES
+.BI "\-s" " topol.tpr" 
+.B Input
+ Run input file: tpr tpb tpa 
+
+.BI "\-o" " error.out" 
+.B Output
+ Generic output file 
+
+.BI "\-so" " tuned.tpr" 
+.B Output, Opt.
+ Run input file: tpr tpb tpa 
+
+.SH OTHER OPTIONS
+.BI "\-[no]h"  "no    "
+ Print help info and quit
+
+.BI "\-[no]version"  "no    "
+ Print version info and quit
+
+.BI "\-nice"  " int" " 0" 
+ Set the nicelevel
+
+.BI "\-beta"  " real" " \-1    " 
+ If positive, overwrite ewald_beta from \fB .tpr\fR file with this value
+
+.BI "\-[no]tune"  "no    "
+ Tune the splitting parameter such that the error is equally distributed between real and reciprocal space
+
+.BI "\-self"  " real" " 1     " 
+ If between 0.0 and 1.0, determine self interaction error from just this fraction of the charged particles
+
+.BI "\-seed"  " int" " 0" 
+ Random number seed used for Monte Carlo algorithm when \fB \-self\fR is set to a value between 0.0 and 1.0
+
+.BI "\-[no]v"  "no    "
+ Be loud and noisy
+
+.SH SEE ALSO
+.BR gromacs(7)
+
+More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.