Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
GROMACS(7)			GROMACS	Manual			    GROMACS(7)

NAME
       gromacs - molecular dynamics simulation suite

DESCRIPTION
       GROMACS (the Groningen Machine for Chemical Simulations)	is a full-fea-
       tured suite of programs to perform molecular dynamics simulations - in
       other words, to simulate	the behavior of	systems	with hundreds to mil-
       lions of	particles, using Newtonian equations of	motion.	 It is primar-
       ily used	for research on	proteins, lipids, and polymers,	but can	be ap-
       plied to	a wide variety of chemical and biological research questions.

SYNOPSIS
       The following commands make up the GROMACS suite.  Please refer to
       their individual	man pages for further details.

       Trajectory analysis

	 gmx-gangle    Calculate angles
	 gmx-distance  Calculate distances between pairs of positions
	 gmx-freevolumeCalculate free volume
	 gmx-sasa      Compute solvent accessible surface area
	 gmx-select    Print general information about selections

       Generating topologies and coordinates

	 gmx-editconf  Edit the	box and	write subgroups
	 gmx-protonate Protonate structures
	 gmx-x2top     Generate	a primitive topology from coordinates
	 gmx-solvate   Solvate a system
	 gmx-insert-moleculesInsert molecules into existing vacancies
	 gmx-genconf   Multiply	a conformation in 'random' orientations
	 gmx-genion    Generate	monoatomic ions	on energetically favorable positions
	 gmx-genrestr  Generate	position restraints or distance	restraints for index groups
	 gmx-pdb2gmx   Convert coordinate files	to topology and	FF-compliant coordinate	files

       Running a simulation

	 gmx-grompp    Make a run input	file
	 gmx-mdrun     Perform a simulation, do	a normal mode analysis or an energy minimization
	 gmx-convert-tprMake a modifed run-input file

       Viewing trajectories

	 gmx-nmtraj    Generate	a virtual oscillating trajectory from an eigenvector
	 gmx-view      View a trajectory on an X-Windows terminal

       Processing energies

	 gmx-enemat    Extract an energy matrix	from an	energy file
	 gmx-energy    Writes energies to xvg files and	display	averages
	 gmx-mdrun     (Re)calculate energies for trajectory frames with -rerun

       Converting files

	 gmx-editconf  Convert and manipulates structure files
	 gmx-eneconv   Convert energy files
	 gmx-sigeps    Convert c6/12 or	c6/cn combinations to and from sigma/epsilon
	 gmx-trjcat    Concatenate trajectory files
	 gmx-trjconv   Convert and manipulates trajectory files
	 gmx-xpm2ps    Convert XPM (XPixelMap) matrices	to postscript or XPM

       Tools

	 gmx-analyze   Analyze data sets
	 gmx-dyndom    Interpolate and extrapolate structure rotations
	 gmx-filter    Frequency filter	trajectories, useful for making	smooth movies
	 gmx-lie       Estimate	free energy from linear	combinations
	 gmx-morph     Interpolate linearly between conformations
	 gmx-pme_error Estimate	the error of using PME with a given input file
	 gmx-sham      Compute free energies or	other histograms from histograms
	 gmx-spatial   Calculate the spatial distribution function
	 gmx-traj      Plot x, v, f, box, temperature and rotational energy from trajectories
	 gmx-tune_pme  Time mdrun as a function	of PME ranks to	optimize settings
	 gmx-wham      Perform weighted	histogram analysis after umbrella sampling
	 gmx-check     Check and compare files
	 gmx-dump      Make binary files human readable
	 gmx-make_ndx  Make index files
	 gmx-mk_angndx Generate	index files for	'gmx angle'
	 gmx-trjorder  Order molecules according to their distance to a	group
	 gmx-xpm2ps    Convert XPM (XPixelMap) matrices	to postscript or XPM

       Distances between structures

	 gmx-cluster   Cluster structures
	 gmx-confrms   Fit two structures and calculates the RMSD
	 gmx-rms       Calculate RMSDs with a reference	structure and RMSD matrices
	 gmx-rmsf      Calculate atomic	fluctuations

       Distances in structures over time

	 gmx-mindist   Calculate the minimum distance between two groups
	 gmx-mdmat     Calculate residue contact maps
	 gmx-polystat  Calculate static	properties of polymers
	 gmx-rmsdist   Calculate atom pair distances averaged with power -2, -3	or -6

       Mass distribution properties over time

	 gmx-gyrate    Calculate the radius of gyration
	 gmx-msd       Calculates mean square displacements
	 gmx-polystat  Calculate static	properties of polymers
	 gmx-rdf       Calculate radial	distribution functions
	 gmx-rotacf    Calculate the rotational	correlation function for molecules
	 gmx-rotmat    Plot the	rotation matrix	for fitting to a reference structure
	 gmx-sans      Compute small angle neutron scattering spectra
	 gmx-saxs      Compute small angle X-ray scattering spectra
	 gmx-traj      Plot x, v, f, box, temperature and rotational energy from trajectories
	 gmx-vanhove   Compute Van Hove	displacement and correlation functions

       Analyzing bonded	interactions

	 gmx-angle     Calculate distributions and correlations	for angles and dihedrals
	 gmx-mk_angndx Generate	index files for	'gmx angle'

       Structural properties

	 gmx-anadock   Cluster structures from Autodock	runs
	 gmx-bundle    Analyze bundles of axes,	e.g., helices
	 gmx-clustsize Calculate size distributions of atomic clusters
	 gmx-disre     Analyze distance	restraints
	 gmx-hbond     Compute and analyze hydrogen bonds
	 gmx-order     Compute the order parameter per atom for	carbon tails
	 gmx-principal Calculate principal axes	of inertia for a group of atoms
	 gmx-rdf       Calculate radial	distribution functions
	 gmx-saltbr    Compute salt bridges
	 gmx-sorient   Analyze solvent orientation around solutes
	 gmx-spol      Analyze solvent dipole orientation and polarization around solutes

       Kinetic properties

	 gmx-bar       Calculate free energy difference	estimates through Bennett's acceptance ratio
	 gmx-current   Calculate dielectric constants and current autocorrelation function
	 gmx-dos       Analyze density of states and properties	based on that
	 gmx-dyecoupl  Extract dye dynamics from trajectories
	 gmx-principal Calculate principal axes	of inertia for a group of atoms
	 gmx-tcaf      Calculate viscosities of	liquids
	 gmx-traj      Plot x, v, f, box, temperature and rotational energy from trajectories
	 gmx-vanhove   Compute Van Hove	displacement and correlation functions
	 gmx-velacc    Calculate velocity autocorrelation functions

       Electrostatic properties

	 gmx-current   Calculate dielectric constants and current autocorrelation function
	 gmx-dielectricCalculate frequency dependent dielectric	constants
	 gmx-dipoles   Compute the total dipole	plus fluctuations
	 gmx-potential Calculate the electrostatic potential across the	box
	 gmx-spol      Analyze solvent dipole orientation and polarization around solutes
	 gmx-genion    Generate	monoatomic ions	on energetically favorable positions

       Protein-specific	analysis

	 gmx-do_dssp   Assign secondary	structure and calculate	solvent	accessible surface area
	 gmx-chi       Calculate everything you	want to	know about chi and other dihedrals
	 gmx-helix     Calculate basic properties of alpha helices
	 gmx-helixorientCalculate local	pitch/bending/rotation/orientation inside helices
	 gmx-rama      Compute Ramachandran plots
	 gmx-wheel     Plot helical wheels

       Interfaces

	 gmx-bundle    Analyze bundles of axes,	e.g., helices
	 gmx-density   Calculate the density of	the system
	 gmx-densmap   Calculate 2D planar or axial-radial density maps
	 gmx-densorder Calculate surface fluctuations
	 gmx-h2order   Compute the orientation of water	molecules
	 gmx-hydorder  Compute tetrahedrality parameters around	a given	atom
	 gmx-order     Compute the order parameter per atom for	carbon tails
	 gmx-potential Calculate the electrostatic potential across the	box

       Covariance analysis

	 gmx-anaeig    Analyze the eigenvectors
	 gmx-covar     Calculate and diagonalize the covariance	matrix
	 gmx-make_edi  Generate	input files for	essential dynamics sampling

       Normal modes

	 gmx-anaeig    Analyze the normal modes
	 gmx-nmeig     Diagonalize the Hessian for normal mode analysis
	 gmx-nmtraj    Generate	a virtual oscillating trajectory from an eigenvector
	 gmx-nmens     Generate	an ensemble of structures from the normal modes
	 gmx-grompp    Make a run input	file
	 gmx-mdrun     Find a potential	energy minimum and calculate the Hessian

ADDITIONAL DOCUMENTATION
       Consult the manual at <http://www.gromacs.org/content/view/27/42/> for
       an introduction to molecular dynamics in	general	and GROMACS in partic-
       ular, as	well as	an overview of the individual programs.

       The shorter HTML	reference is available in /usr/share/doc/gromacs/html/
       .

REFERENCES
       The development of GROMACS is mainly funded by academic research
       grants.	To help	us fund	development, the authors humbly	ask that you
       cite the	GROMACS	papers:

       H.J.C. Berendsen, D. van	der Spoel and R. van Drunen.  GROMACS: A mes-
       sage-passing parallel molecular dynamics	implementation.	 Comp. Phys.
       Comm. 91, 43-56 (1995)

       Erik Lindahl, Berk Hess and David van der Spoel.	 GROMACS 3.0: A	pack-
       age for molecular simulation and	trajectory analysis.  J. Mol. Mod. 7,
       306-317 (2001)

       B. Hess,	C. Kutzner, D. van der Spoel, and E. Lindahl.  GROMACS 4: Al-
       gorithms	for Highly Efficient, Load-Balanced, and Scalable Molecular
       Simulation.  J. Chem. Theory Comput. 4, 3, 435-447 (2008),
       <http://dx.doi.org/10.1021/ct700301q>

AUTHORS
       Current developers:

       David van der Spoel <spoel@gromacs.org>
       Berk Hess <hess@gromacs.org>
       Erik Lindahl <lindahl@gromacs.org>

       A full list of present and former contributors is available at
       <http://www.gromacs.org>

       This manual page	is largely based on the	GROMACS	online reference, and
       was prepared in this format by Nicholas Breen <nbreen@ofb.net>.

BUGS
       GROMACS has no major known bugs,	but be warned that it stresses your
       CPU more	than most software.  Systems with slightly flaky hardware may
       prove unreliable	while running heavy-duty simulations.  If at all pos-
       sible, please try to reproduce bugs on another machine before reporting
       them.

VERSION	5.0.6							    GROMACS(7)

NAME | DESCRIPTION | SYNOPSIS | ADDITIONAL DOCUMENTATION | REFERENCES | AUTHORS | BUGS

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=gromacs&sektion=7&manpath=FreeBSD+12.0-RELEASE+and+Ports>

home | help