GROMACS |
Author |
Written by: Berk Hess, David van der Spoel, and Erik Lindahl. Additional contributions by: |
Origin |
Copyright 1991-2000: Department of Biophysical Chemistry, University of Groningen. Nijenborgh 4, 9747 AG Groningen, The Netherlands. Copyright 2001-2010: The GROMACS development team at the Royal Institute of Technology and Uppsala University, Sweden. |
Version |
GROMACS Version 4.5.4 & 4.0.5 |
Official Web Site |
Brief Program Description |
GROMACS is a molecular dynamics package primarily designed for studying biochemical molecules, such as proteins and lipids, but can also be used on non-biological systems, such as polymers. The following list gives a brief description of the programs available with this version of GROMACS. For more information, users are referred to the User Manual. 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 genbox solvates a system genion generates mono atomic ions on energetically favorable positions genconf multiplies a conformation in random orientations genprestr generates position restraints or distance restraints for index groups g_protonate protonates structures RUNNING A SIMULATION grompp makes a run input file tpbconv makes a run input file for restarting a crashed run mdrun performs a simulation VIEWING TRAJECTORIES ngmx displays a trajectory g_nmtraj generate a virtual trajectory from an eigenvector PROCESSING ENERGIES g_energy writes energies to xvg files and displays averages g_enemat extracts an energy matrix from an energy file mdrun with -rerun (re)calculates energies for trajectory frames CONVERTING FILES editconf converts and manipulates structure files trjconv converts and manipulates trajectory files trjcat concatenates trajectory files eneconv converts energy files xmp2ps converts XPM matrices to encapsulated postscript (or XPM) g_sigeps convert c6/12 or c6/cn combinations to and from sigma/epsilon 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 g_sham makes multi-dimensional free-energy, enthalpy and entropy plots trjorder orders molecules according to their distance to a group 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_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_tune_pme time mdrun as a function of PME nodes to optimize settings 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_rmsf calculates atomic fluctuations 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_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 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_rotacf calculates the rotational correlation function for molecules g_vanhove calculates Van Hove displacement functions g_polystat calculates static properties of polymers g_rdf calculates radial distribution functions g_rotmat plots the rotation matrix for fitting to a reference structure 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_dih analyzes dihedral transitions STRUCTURAL PROPERTIES 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 solvent distribution functions 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 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 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_spol analyze dipoles around a solute 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 INTERFACES g_potential calculates the electrostatic potential across the box g_density calculates the density of the system 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_densmap calculates 2D planar or axial-radial density maps g_bundle analyzes bundles of axes, e.g. transmembrane helices g_membed embeds a protein into a lipid bilayer COVARIANCE ANALYSIS g_covar calculates and diagonalizes the covariance matrix g_anaeig analyzes the eigenvectors make_edi generate input files for essential dynamics sampling NORMAL MODES grompp makes a run input file mdrun finds a potential energy minimum mdrun calculates the Hessian g_nmeig diagonalizes the Hessian g_anaeig analyzes the normal modes g_nmens generates an ensemble of structures from the normal modes g_nmtraj generate oscillating trajectory of an eigenmode |
Areas of Application |
The main advantage of the package is that the calculation of the non-bonded interactions is extremely fast which allows systems with hundreds to millions of particles to be simulated. For recent changes to the package, please visit the GROMACS website. |
Implementation and Access |
The command $CHEM/rungromacs454 accesses and executes the computational chemistry program GROMACS version 4.5.4 on Magellan and runs in serial or parallel. Please note that only the molecular dynamics simulation program mdrun is parallelised in the parallel version. Access is via the command rungromacs as shown: $CHEM/rungromacs454 progname options where progname stands for the name of one of the programs listed and options are specific options for each program. Users are advised to check the user manual prior to submitting jobs set up using older version of GROMACS as there have been many changes made between versions. The previous version 4.0.5 is still available via the command $CHEM/rungromacs405. |
Machines |
Available on Magellan. |
Documentation |
Documentation for GROMACS is available from the directory $CHEM/doc/gromacs in PDF format or can be downloaded directly from the GROMACS web site. GROMACS examples are located in the directory $CHEM/doc/gromacs/examples. Tutorials explaining how to run simulations for these examples can be found on the GROMACS web site.
There are Unix-style man pages containing information on the local implementation of GROMACS, accessible by typing: man rungromacs454 for version 4.5.4 and man rungromacs405 for version 4.0.5. |
Literature References |
References are listed in the Gromacs User Manual version, http://www.gromacs.org. |
Specialist Support |
Dr Helen Tsui. Address: Department of Chemistry, Imperial College London, South Kensington, London SW7 2AZ. Tel: 020 7594 1220 Email: helen.tsui@imperial.ac.uk. |
Program Restrictions and Comments |
N/A |