1GROMACS(7) GROMACS suite, Version 4.0 GROMACS(7)
2
6 gromacs - molecular dynamics simulation suite
7
9 GROMACS (the Groningen Machine for Chemical Simulations) is a full-fea‐
10 tured suite of programs to perform molecular dynamics simulations - in
11 other words, to simulate the behavior of systems with hundreds to mil‐
12 lions of particles, using Newtonian equations of motion. It is primar‐
13 ily used for research on proteins, lipids, and polymers, but can be
14 applied to a wide variety of chemical and biological research ques‐
15 tions.
16
18 The following commands make up the GROMACS suite. Please refer to
19 their individual man pages for further details.
20 Generating topologies and coordinates
22 pdb2gmx converts pdb files to topology and coordinate files
24 g_x2top generates a primitive topology from coordinates
25 editconf edits the box and writes subgroups
26 genbox solvates a system
27 genion generates mono atomic ions on energetically favorable positions
28 genconf multiplies a conformation in 'random' orientations
29 g_protonate protonates structures
30 Running a simulation
32 grompp makes a run input file
34 tpbconv makes a run input file for restarting a crashed run
35 mdrun performs a simulation, do a normal mode analysis or an energy minimization
36 mdrun_mpi performs a sim across multiple CPUs or systems
37 Viewing trajectories
39 ngmx displays a trajectory
41 g_highway X Window System gadget for highway simulations
42 g_nmtraj generate a virtual trajectory from an eigenvector
43 Processing energies
45 g_energy writes energies to xvg files and displays averages
47 g_enemat extracts an energy matrix from an energy file
48 mdrun with -rerun (re)calculates energies for trajectory frames
49 Converting files
51 editconf converts and manipulates structure files
53 trjconv converts and manipulates trajectory files
54 trjcat concatenates trajectory files
55 eneconv converts energy files
56 xpm2ps converts XPM matrices to encapsulated postscript (or XPM)
57 g_sigeps convert c6/12 or c6/cn combinations to and from sigma/epsilon
58 Tools
60 make_ndx makes index files
62 mk_angndx generates index files for g_angle
63 gmxcheck checks and compares files
64 gmxdump makes binary files human readable
65 g_traj plots x, v and f of selected atoms/groups (and more) from a trajectory
66 g_analyze analyzes data sets
67 trjorder orders molecules according to their distance to a group
68 g_filter frequency filters trajectories, useful for making smooth movies
69 g_lie free energy estimate from linear combinations
70 g_dyndom interpolate and extrapolate structure rotations
71 g_morph linear interpolation of conformations
72 g_wham weighted histogram analysis after umbrella sampling
73 xpm2ps convert XPM (XPixelMap) file to postscript
74 g_sham read/write xmgr and xvgr data sets
75 g_spatial calculates the spatial distribution function (more control than g_sdf)
76 g_sdf calculates the spatial distribution function (faster than g_spatial)
77 g_select selects groups of atoms based on flexible textual selections
78 g_tune_pme time mdrun as a function of PME nodes to optimize settings
79 Distances between structures
81 g_rms calculates rmsd's with a reference structure and rmsd matrices
83 g_confrms fits two structures and calculates the rmsd
84 g_cluster clusters structures
85 g_rmsf calculates atomic fluctuations
86 Distances in structures over time
88 g_mindist calculates the minimum distance between two groups
90 g_dist calculates the distances between the centers of mass of two groups
91 g_bond calculates distances between atoms
92 g_mdmat calculates residue contact maps
93 g_polystat calculates static properties of polymers
94 g_rmsdist calculates atom pair distances averaged with power -2, -3 or -6
95 Mass distribution properties over time
97 g_traj plots x, v, f, box, temperature and rotational energy
99 g_gyrate calculates the radius of gyration
100 g_msd calculates mean square displacements
101 g_polystat calculates static properties of polymers
102 g_rotacf calculates the rotational correlation function for molecules
103 g_rdf calculates radial distribution functions
104 g_rotmat plots the rotation matrix for fitting to a reference structure
105 g_vanhove calculates Van Hove displacement functions
106 Analyzing bonded interactions
108 g_bond calculates bond length distributions
110 mk_angndx generates index files for g_angle
111 g_angle calculates distributions and correlations for angles and dihedrals
112 g_dih analyzes dihedral transitions
113 Structural properties
115 g_hbond computes and analyzes hydrogen bonds
117 g_saltbr computes salt bridges
118 g_sas computes solvent accessible surface area
119 g_order computes the order parameter per atom for carbon tails
120 g_principal calculates axes of inertia for a group of atoms
121 g_rdf calculates radial distribution functions
122 g_sdf calculates solvent distribution functions
123 g_sgangle computes the angle and distance between two groups
124 g_sorient analyzes solvent orientation around solutes
125 g_spol analyzes solvent dipole orientation and polarization around solutes
126 g_bundle analyzes bundles of axes, e.g. helices
127 g_disre analyzes distance restraints
128 g_clustsize calculate size distributions of atomic clusters
129 g_anadock cluster structures from Autodock runs
130 Kinetic properties
132 g_traj plots x, v, f, box, temperature and rotational energy
134 g_velacc calculates velocity autocorrelation functions
135 g_tcaf calculates viscosities of liquids
136 g_kinetics calculate kinetic rate constants (experimental)
137 g_bar calculates free energy difference estimates through Bennett's acceptance ratio
138 g_current calculate current autocorrelation function of system
139 g_vanhove compute Van Hove correlation function
140 g_principal calculate principal axes of inertion for a group of atoms
141 Electrostatic properties
143 genion generates mono atomic ions on energetically favorable positions
145 g_potential calculates the electrostatic potential across the box
146 g_dipoles computes the total dipole plus fluctuations
147 g_dielectric calculates frequency dependent dielectric constants
148 g_current calculate current autocorrelation function of system
149 g_spol analyze dipoles around a solute
150 Protein specific analysis
152 do_dssp assigns secondary structure and calculates solvent accessible surface area
154 g_chi calculates everything you want to know about chi and other dihedrals
155 g_helix calculates everything you want to know about helices
156 g_helixorient calculate coordinates/directions of alpha-helix components
157 g_rama computes Ramachandran plots
158 g_xrama shows animated Ramachandran plots
159 wheel plots helical wheels
160 Interfaces
162 g_potential calculates the electrostatic potential across the box
164 g_density calculates the density of the system
165 g_order computes the order parameter per atom for carbon tails
166 g_h2order computes the orientation of water molecules
167 g_bundle analyzes bundles of axes, e.g. transmembrane helices
168 g_membed embeds a protein into a lipid bilayer
169 Covariance analysis
171 g_covar calculates and diagonalizes the covariance matrix
173 g_anaeig analyzes the eigenvectors
174 make_edi generate essential-dynamics input file from g_covar output
175 Normal modes
177 grompp makes a run input file
179 mdrun finds a potential energy minimum
180 mdrun calculates the Hessian
181 g_nmeig diagonalizes the Hessian
182 make_edi generates essential-dynamics input file from g_nmeig analysis
183 g_anaeig analyzes the normal modes
184 g_nmens generates an ensemble of structures from the normal modes
185
187 Consult the manual at <http://www.gromacs.org/content/view/27/42/> for
188 an introduction to molecular dynamics in general and GROMACS in partic‐
189 ular, as well as an overview of the individual programs.
190 The shorter HTML reference and GROMACS FAQ are available in
192 /usr/share/doc/gromacs/html/ .
193 Tutorial files and other miscellaneous references are stored in
195 /usr/share/gromacs/ .
196
198 The development of GROMACS is mainly funded by academic research
199 grants. To help us fund development, the authors humbly ask that you
200 cite the GROMACS papers:
201 H.J.C. Berendsen, D. van der Spoel and R. van Drunen. GROMACS: A mes‐
203 sage-passing parallel molecular dynamics implementation. Comp. Phys.
204 Comm. 91, 43-56 (1995)
205 Erik Lindahl, Berk Hess and David van der Spoel. GROMACS 3.0: A pack‐
207 age for molecular simulation and trajectory analysis. J. Mol. Mod. 7,
208 306-317 (2001)
209 B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl. GROMACS 4:
211 Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular
212 Simulation. J. Chem. Theory Comput. 4, 3, 435-447 (2008),
213 <http://dx.doi.org/10.1021/ct700301q>
214
216 Current developers:
217 David van der Spoel <spoel@gromacs.org>
219 Berk Hess <hess@gromacs.org>
220 Erik Lindahl <lindahl@gromacs.org>
221 A full list of present and former contributors is available at
223 <http://www.gromacs.org>
224 This manual page is largely based on the GROMACS online reference, and
226 was prepared in this format by Nicholas Breen <nbreen@ofb.net>.
227
229 GROMACS has no major known bugs, but be warned that it stresses your
230 CPU more than most software. Systems with slightly flaky hardware may
231 prove unreliable while running heavy-duty simulations. If at all pos‐
232 sible, please try to reproduce bugs on another machine before reporting
233 them.
234gromacs 2008-10-12 GROMACS(7)