Package gromacs-common

GROMACS shared data and documentation

http://www.gromacs.org

GROMACS is a versatile and extremely well optimized package to perform
molecular dynamics computer simulations and subsequent trajectory analysis.
It is developed for biomolecules like proteins, but the extremely high
performance means it is used also in several other field like polymer chemistry
and solid state physics.

This package includes architecture independent data and HTML documentation.

General Commands (Section 1)
gmx
GROMACS is a full-featured suite of programs to perform molecular dynamics simulations, i.e., to simulate the behavior of systems with hundreds to millions of...
gmx-anadock
gmx anadock analyses the results of an Autodock run and clusters the structures together, based on distance or RMSD. The docked energy and free energy estimates...
gmx-anaeig
gmx anaeig analyzes eigenvectors. The eigenvectors can be of a covariance matrix (gmx covar) or of a Normal Modes analysis (gmx nmeig). When a trajectory is...
gmx-analyze
gmx analyze reads an ASCII file and analyzes data sets. A line in the input file may start with a time (see option -time) and any number of y-values may follow...
gmx-angle
gmx angle computes the angle distribution for a number of angles or dihedrals. With option -ov, you can plot the average angle of a group of angles as a...
gmx-bar
gmx bar calculates free energy difference estimates through Bennett's acceptance ratio method (BAR). It also automatically adds series of individual free...
gmx-bundle
gmx bundle analyzes bundles of axes. The axes can be for instance helix axes. The program reads two index groups and divides both of them in -na parts. The...
gmx-check
gmx check reads a trajectory (.tng, .trr or .xtc), an energy file (.edr) or an index file (.ndx) and prints out useful information about them. Option -c checks...
gmx-chi
gmx chi computes phi, psi, omega, and chi dihedrals for all your amino acid backbone and sidechains. It can compute dihedral angle as a function of time, and as...
gmx-cluster
gmx cluster can cluster structures using several different methods. Distances between structures can be determined from a trajectory or read from an .xpm matrix...
gmx-clustsize
gmx clustsize computes the size distributions of molecular/atomic clusters in the gas phase. The output is given in the form of an .xpm file. The total number...
gmx-confrms
gmx confrms computes the root mean square deviation (RMSD) of two structures after least-squares fitting the second structure on the first one. The two...
gmx-convert-tpr
gmx convert-tpr can edit run input files in four ways. 1. by modifying the number of steps in a run input file with options -extend, -until or -nsteps...
gmx-covar
gmx covar calculates and diagonalizes the (mass-weighted) covariance matrix. All structures are fitted to the structure in the structure file. When this is not...
gmx-current
gmx current is a tool for calculating the current autocorrelation function, the correlation of the rotational and translational dipole moment of the system, and...
gmx-density
gmx density computes partial densities across the box, using an index file. For the total density of NPT simulations, use gmx energy instead. Option -center...
gmx-densmap
gmx densmap computes 2D number-density maps. It can make planar and axial-radial density maps. The output .xpm file can be visualized with for instance xv and...
gmx-densorder
gmx densorder reduces a two-phase density distribution along an axis, computed over a MD trajectory, to 2D surfaces fluctuating in time, by a fit to a...
gmx-dielectric
gmx dielectric calculates frequency dependent dielectric constants from the autocorrelation function of the total dipole moment in your simulation. This ACF can...
gmx-dipoles
gmx dipoles computes the total dipole plus fluctuations of a simulation system. From this you can compute e.g. the dielectric constant for low-dielectric media...
gmx-disre
gmx disre computes violations of distance restraints. The program always computes the instantaneous violations rather than time-averaged, because this analysis...
gmx-distance
gmx distance calculates distances between pairs of positions as a function of time. Each selection specifies an independent set of distances to calculate. Each...
gmx-do_dssp
gmx do_dssp reads a trajectory file and computes the secondary structure for each time frame calling the dssp program. If you do not have the dssp program, get...
gmx-dos
gmx dos computes the Density of States from a simulations. In order for this to be meaningful the velocities must be saved in the trajecotry with sufficiently...
gmx-dump
gmx dump reads a run input file (.tpr), a trajectory (.trr/.xtc//tng), an energy file (.edr) or a checkpoint file (.cpt) and prints that to standard output in a...
gmx-dyecoupl
gmx dyecoupl extracts dye dynamics from trajectory files. Currently, R and kappa^2 between dyes is extracted for (F)RET simulations with assumed dipolar...
gmx-dyndom
gmx dyndom reads a .pdb file output from DynDom (http://www.cmp.uea.ac.uk/dyndom/). It reads the coordinates, the coordinates of the rotation axis, and an index...
gmx-editconf
gmx editconf converts generic structure format to .gro, .g96 or .pdb. The box can be modified with options -box, -d and -angles. Both -box and -d will center...
gmx-eneconv
With multiple files specified for the -f option: Concatenates several energy files in sorted order. In the case of double time frames, the one in the later file...
gmx-enemat
gmx enemat extracts an energy matrix from the energy file (-f). With -groups a file must be supplied with on each line a group of atoms to be used. For these...
gmx-energy
gmx energy extracts energy components or distance restraint data from an energy file. The user is prompted to interactively select the desired energy terms...
gmx-filter
gmx filter performs frequency filtering on a trajectory. The filter shape is cos(pi t/A) + 1 from -A to +A, where A is given by the option -nf times the time...
gmx-freevolume
gmx freevolume calculates the free volume in a box as a function of time. The free volume is plotted as a fraction of the total volume. The program tries to...
gmx-gangle
gmx gangle computes different types of angles between vectors. It supports both vectors defined by two positions and normals of planes defined by three...
gmx-genconf
gmx genconf multiplies a given coordinate file by simply stacking them on top of each other, like a small child playing with wooden blocks. The program makes a...
gmx-genion
gmx genion randomly replaces solvent molecules with monoatomic ions. The group of solvent molecules should be continuous and all molecules should have the same...
gmx-genrestr
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-direction based on the...
gmx-grompp
gmx grompp (the gromacs preprocessor) reads a molecular topology file, checks the validity of the file, expands the topology from a molecular description to an...
gmx-gyrate
gmx gyrate computes the radius of gyration of a molecule and the radii of gyration about the x-, y- and z-axes, as a function of time. The atoms are explicitly...
gmx-h2order
gmx h2order computes the orientation of water molecules with respect to the normal of the box. The program determines the average cosine of the angle between...
gmx-hbond
gmx hbond computes and analyzes hydrogen bonds. Hydrogen bonds are determined based on cutoffs for the angle Hydrogen - Donor - Acceptor (zero is extended) and...
gmx-helix
gmx helix computes all kinds of helix properties. First, the peptide is checked to find the longest helical part, as determined by hydrogen bonds and phi/psi...
gmx-helixorient
gmx helixorient calculates the coordinates and direction of the average axis inside an alpha helix, and the direction/vectors of both the Calpha and...
gmx-help
gmx(1) More information about GROMACS is available at <http://www.gromacs.org/>.
gmx-hydorder
gmx hydorder computes the tetrahedrality order parameters around a given atom. Both angle an distance order parameters are calculated. See P.-L. Chau and A.J...
gmx-insert-molecules
gmx insert-molecules inserts -nmol copies of the system specified in the -ci input file. The insertions take place either into vacant space in the solute...
gmx-lie
gmx lie computes a free energy estimate based on an energy analysis from nonbonded energies. One needs an energy file with the following components: Coul-(A-B)...
gmx-make_edi
gmx make_edi generates an essential dynamics (ED) sampling input file to be used with mdrun based on eigenvectors of a covariance matrix (gmx covar) or from a...
gmx-make_ndx
Index groups are necessary for almost every GROMACS program. All these programs can generate default index groups. You ONLY have to use gmx make_ndx when you...
gmx-mdmat
gmx mdmat makes distance matrices consisting of the smallest distance between residue pairs. With -frames, these distance matrices can be stored in order to see...
gmx-mdrun
gmx mdrun is the main computational chemistry engine within GROMACS. Obviously, it performs Molecular Dynamics simulations, but it can also perform Stochastic...
gmx-mindist
gmx 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...
gmx-mk_angndx
gmx mk_angndx makes an index file for calculation of angle distributions etc. It uses a run input file (.tpx) for the definitions of the angles, dihedrals etc.
gmx-morph
gmx morph does a linear interpolation of conformations in order to create intermediates. Of course these are completely unphysical, but that you may try to...
gmx-msd
gmx msd computes the mean square displacement (MSD) of atoms from a set of initial positions. This provides an easy way to compute the diffusion constant using...
gmx-nmeig
gmx nmeig calculates the eigenvectors/values of a (Hessian) matrix, which can be calculated with gmx mdrun. The eigenvectors are written to a trajectory file...
gmx-nmens
gmx nmens generates an ensemble around an average structure in a subspace that is defined by a set of normal modes (eigenvectors). The eigenvectors are assumed...
gmx-nmtraj
gmx nmtraj generates an virtual trajectory from an eigenvector, corresponding to a harmonic Cartesian oscillation around the average structure. The eigenvectors...
gmx-order
gmx order computes the order parameter per atom for carbon tails. For atom i the vector i-1, i+1 is used together with an axis. The index file should contain...
gmx-pairdist
gmx pairdist calculates pairwise distances between one reference selection (given with -ref) and one or more other selections (given with -sel). It can...
gmx-pdb2gmx
gmx pdb2gmx reads a .pdb (or .gro) file, reads some database files, adds hydrogens to the molecules and generates coordinates in GROMACS (GROMOS), or optionally...
gmx-pme_error
gmx pme_error estimates the error of the electrostatic forces if using the sPME algorithm. The flag -tune will determine the splitting parameter such that the...
gmx-polystat
gmx polystat plots static properties of polymers as a function of time and prints the average. By default it determines the average end-to-end distance and...
gmx-potential
gmx potential computes the electrostatical potential across the box. The potential is calculated by first summing the charges per slice and then integrating...
gmx-principal
gmx principal calculates the three principal axes of inertia for a group of atoms. NOTE: Old versions of GROMACS wrote the output data in a strange transposed...
gmx-rama
gmx rama selects the phi/psi dihedral combinations from your topology file and computes these as a function of time. Using simple Unix tools such as grep you...
gmx-rdf
gmx rdf calculates radial distribution functions from one reference set of position (set with -ref) to one or more sets of positions (set with -sel). To compute...
gmx-rms
gmx rms compares two structures by computing the root mean square deviation (RMSD), the size-independent rho similarity parameter (rho) or the scaled rho...
gmx-rmsdist
gmx rmsdist computes the root mean square deviation of atom distances, which has the advantage that no fit is needed like in standard RMS deviation as computed...
gmx-rmsf
gmx rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions in the trajectory (supplied with -f) after (optionally)...
gmx-rotacf
gmx rotacf calculates the rotational correlation function for molecules. Atom triplets (i,j,k) must be given in the index file, defining two vectors ij and jk...
gmx-rotmat
gmx rotmat plots the rotation matrix required for least squares fitting a conformation onto the reference conformation provided with -s. Translation is removed...
gmx-saltbr
gmx saltbr plots the distance between all combination of charged groups as a function of time. The groups are combined in different ways. A minimum distance can...
gmx-sans
gmx sans computes SANS spectra using Debye formula. It currently uses topology file (since it need to assigne element for each atom). Parameters: -pr Computes...
gmx-sasa
gmx sasa computes solvent accessible surface areas. See Eisenhaber F, Lijnzaad P, Argos P, Sander C, & Scharf M (1995) J. Comput. Chem. 16, 273-284 for the...
gmx-saxs
gmx saxs calculates SAXS structure factors for given index groups based on Cromer's method. Both topology and trajectory files are required.
gmx-select
gmx select writes out basic data about dynamic selections. It can be used for some simple analyses, or the output can be combined with output from other...
gmx-sham
gmx sham makes multi-dimensional free-energy, enthalpy and entropy plots. gmx sham reads one or more .xvg files and analyzes data sets. The basic purpose of gmx...
gmx-sigeps
gmx sigeps is a simple utility that converts C6/C12 or C6/Cn combinations to sigma and epsilon, or vice versa. It can also plot the potential in file. In...
gmx-solvate
gmx solvate can do one of 2 things: 1) Generate a box of solvent. Specify -cs and -box. Or specify -cs and -cp with a structure file with a box, but without...
gmx-sorient
gmx sorient analyzes solvent orientation around solutes.
gmx-spatial
gmx spatial calculates the spatial distribution function and outputs it in a form that can be read by VMD as Gaussian98 cube format. For a system of 32,000...
gmx-spol
gmx spol analyzes dipoles around a solute; it is especially useful for polarizable water. A group of reference atoms, or a center of mass reference (option...
gmx-tcaf
gmx tcaf computes tranverse current autocorrelations. These are used to estimate the shear viscosity, eta. For details see: Palmer, Phys. Rev. E 49 (1994) pp...
gmx-traj
gmx traj plots coordinates, velocities, forces and/or the box. With -com the coordinates, velocities and forces are calculated for the center of mass of each...
gmx-trjcat
gmx trjcat concatenates several input trajectory files in sorted order. In case of double time frames the one in the later file is used. By specifying -settime...
gmx-trjconv
Convert and manipulates trajectory files
gmx-trjorder
gmx trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option -z). With distance ordering, it...
gmx-tune_pme
For a given number -np or -ntmpi of ranks, gmx tune_pme systematically times gmx mdrun with various numbers of PME-only ranks and determines which setting is...
gmx-vanhove
gmx vanhove computes the Van Hove correlation function. The Van Hove G(r,t) is the probability that a particle that is at r_0 at time zero can be found at...
gmx-velacc
gmx velacc computes the velocity autocorrelation function. When the -m option is used, the momentum autocorrelation function is calculated. With option -mol the...
gmx-view
gmx view is the GROMACS trajectory viewer. This program reads a trajectory file, a run input file and an index file and plots a 3D structure of your molecule on...
gmx-wham
gmx wham is an analysis program that implements the Weighted Histogram Analysis Method (WHAM). It is intended to analyze output files generated by umbrella...
gmx-wheel
gmx wheel plots a helical wheel representation of your sequence. The input sequence is in the .dat file where the first line contains the number of residues and...
gmx-x2top
gmx x2top generates a primitive topology from a coordinate file. The program assumes all hydrogens are present when defining the hybridization from the atom...
gmx-xpm2ps
gmx xpm2ps makes a beautiful color plot of an XPixelMap file. Labels and axis can be displayed, when they are supplied in the correct matrix format. Matrix data...