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130 .\" ========================================================================
132 .IX Title "GROMACS 7"
133 .TH GROMACS 7 "2008-10-12" "gromacs" "GROMACS suite, Version 4.0"
135 gromacs \- molecular dynamics simulation suite
138 (the Groningen Machine for Chemical Simulations) is a full-featured
139 suite of programs to perform molecular dynamics simulations - in other
140 words, to simulate the behavior of systems with hundreds to millions
141 of particles, using Newtonian equations of motion. It is primarily
142 used for research on proteins, lipids, and polymers, but can be applied
143 to a wide variety of chemical and biological research questions.
145 .IX Header "SYNOPSIS"
147 The following commands make up the GROMACS suite. Please refer to their
148 individual man pages for further details.
149 .Sh "Generating topologies and coordinates"
150 .IX Subsection "Generating topologies and coordinates"
152 \& pdb2gmx converts pdb files to topology and coordinate files
153 \& g_x2top generates a primitive topology from coordinates
154 \& editconf edits the box and writes subgroups
155 \& genbox solvates a system
156 \& genion generates mono atomic ions on energetically favorable positions
157 \& genconf multiplies a conformation in 'random' orientations
158 \& g_protonate protonates structures
160 .Sh "Running a simulation"
161 .IX Subsection "Running a simulation"
163 \& grompp makes a run input file
164 \& tpbconv makes a run input file for restarting a crashed run
165 \& mdrun performs a simulation, do a normal mode analysis or an energy minimization
166 \& mdrun_mpi performs a sim across multiple CPUs or systems
168 .Sh "Viewing trajectories"
169 .IX Subsection "Viewing trajectories"
171 \& ngmx displays a trajectory
172 \& g_highway X Window System gadget for highway simulations
173 \& g_nmtraj generate a virtual trajectory from an eigenvector
175 .Sh "Processing energies"
176 .IX Subsection "Processing energies"
178 \& g_energy writes energies to xvg files and displays averages
179 \& g_enemat extracts an energy matrix from an energy file
180 \& mdrun with \-rerun (re)calculates energies for trajectory frames
182 .Sh "Converting files"
183 .IX Subsection "Converting files"
185 \& editconf converts and manipulates structure files
186 \& trjconv converts and manipulates trajectory files
187 \& trjcat concatenates trajectory files
188 \& eneconv converts energy files
189 \& xpm2ps converts XPM matrices to encapsulated postscript (or XPM)
190 \& g_sigeps convert c6/12 or c6/cn combinations to and from sigma/epsilon
193 .IX Subsection "Tools"
195 \& make_ndx makes index files
196 \& mk_angndx generates index files for g_angle
197 \& gmxcheck checks and compares files
198 \& gmxdump makes binary files human readable
199 \& g_traj plots x, v and f of selected atoms/groups (and more) from a trajectory
200 \& g_analyze analyzes data sets
201 \& trjorder orders molecules according to their distance to a group
202 \& g_filter frequency filters trajectories, useful for making smooth movies
203 \& g_lie free energy estimate from linear combinations
204 \& g_dyndom interpolate and extrapolate structure rotations
205 \& g_morph linear interpolation of conformations
206 \& g_wham weighted histogram analysis after umbrella sampling
207 \& xpm2ps convert XPM (XPixelMap) file to postscript
208 \& g_sham read/write xmgr and xvgr data sets
209 \& g_spatial calculates the spatial distribution function (more control than g_sdf)
210 \& g_sdf calculates the spatial distribution function (faster than g_spatial)
211 \& g_select selects groups of atoms based on flexible textual selections
212 \& g_tune_pme time mdrun as a function of PME nodes to optimize settings
214 .Sh "Distances between structures"
215 .IX Subsection "Distances between structures"
217 \& g_rms calculates rmsd's with a reference structure and rmsd matrices
218 \& g_confrms fits two structures and calculates the rmsd
219 \& g_cluster clusters structures
220 \& g_rmsf calculates atomic fluctuations
222 .Sh "Distances in structures over time"
223 .IX Subsection "Distances in structures over time"
225 \& g_mindist calculates the minimum distance between two groups
226 \& g_dist calculates the distances between the centers of mass of two groups
227 \& g_bond calculates distances between atoms
228 \& g_mdmat calculates residue contact maps
229 \& g_polystat calculates static properties of polymers
230 \& g_rmsdist calculates atom pair distances averaged with power \-2, \-3 or \-6
232 .Sh "Mass distribution properties over time"
233 .IX Subsection "Mass distribution properties over time"
235 \& g_traj plots x, v, f, box, temperature and rotational energy
236 \& g_gyrate calculates the radius of gyration
237 \& g_msd calculates mean square displacements
238 \& g_polystat calculates static properties of polymers
239 \& g_rotacf calculates the rotational correlation function for molecules
240 \& g_rdf calculates radial distribution functions
241 \& g_rotmat plots the rotation matrix for fitting to a reference structure
242 \& g_vanhove calculates Van Hove displacement functions
244 .Sh "Analyzing bonded interactions"
245 .IX Subsection "Analyzing bonded interactions"
247 \& g_bond calculates bond length distributions
248 \& mk_angndx generates index files for g_angle
249 \& g_angle calculates distributions and correlations for angles and dihedrals
250 \& g_dih analyzes dihedral transitions
252 .Sh "Structural properties"
253 .IX Subsection "Structural properties"
255 \& g_hbond computes and analyzes hydrogen bonds
256 \& g_saltbr computes salt bridges
257 \& g_sas computes solvent accessible surface area
258 \& g_order computes the order parameter per atom for carbon tails
259 \& g_principal calculates axes of inertia for a group of atoms
260 \& g_rdf calculates radial distribution functions
261 \& g_sdf calculates solvent distribution functions
262 \& g_sgangle computes the angle and distance between two groups
263 \& g_sorient analyzes solvent orientation around solutes
264 \& g_spol analyzes solvent dipole orientation and polarization around solutes
265 \& g_bundle analyzes bundles of axes, e.g. helices
266 \& g_disre analyzes distance restraints
267 \& g_clustsize calculate size distributions of atomic clusters
268 \& g_anadock cluster structures from Autodock runs
270 .Sh "Kinetic properties"
271 .IX Subsection "Kinetic properties"
273 \& g_traj plots x, v, f, box, temperature and rotational energy
274 \& g_velacc calculates velocity autocorrelation functions
275 \& g_tcaf calculates viscosities of liquids
276 \& g_kinetics calculate kinetic rate constants (experimental)
277 \& g_bar calculates free energy difference estimates through Bennett's acceptance ratio
278 \& g_current calculate current autocorrelation function of system
279 \& g_vanhove compute Van Hove correlation function
280 \& g_principal calculate principal axes of inertion for a group of atoms
282 .Sh "Electrostatic properties"
283 .IX Subsection "Electrostatic properties"
285 \& genion generates mono atomic ions on energetically favorable positions
286 \& g_potential calculates the electrostatic potential across the box
287 \& g_dipoles computes the total dipole plus fluctuations
288 \& g_dielectric calculates frequency dependent dielectric constants
289 \& g_current calculate current autocorrelation function of system
290 \& g_spol analyze dipoles around a solute
292 .Sh "Protein specific analysis"
293 .IX Subsection "Protein specific analysis"
295 \& do_dssp assigns secondary structure and calculates solvent accessible surface area
296 \& g_chi calculates everything you want to know about chi and other dihedrals
297 \& g_helix calculates everything you want to know about helices
298 \& g_helixorient calculate coordinates/directions of alpha-helix components
299 \& g_rama computes Ramachandran plots
300 \& g_xrama shows animated Ramachandran plots
301 \& wheel plots helical wheels
304 .IX Subsection "Interfaces"
306 \& g_potential calculates the electrostatic potential across the box
307 \& g_density calculates the density of the system
308 \& g_order computes the order parameter per atom for carbon tails
309 \& g_h2order computes the orientation of water molecules
310 \& g_bundle analyzes bundles of axes, e.g. transmembrane helices
311 \& g_membed embeds a protein into a lipid bilayer
313 .Sh "Covariance analysis"
314 .IX Subsection "Covariance analysis"
316 \& g_covar calculates and diagonalizes the covariance matrix
317 \& g_anaeig analyzes the eigenvectors
318 \& make_edi generate essential-dynamics input file from g_covar output
321 .IX Subsection "Normal modes"
323 \& grompp makes a run input file
324 \& mdrun finds a potential energy minimum
325 \& mdrun calculates the Hessian
326 \& g_nmeig diagonalizes the Hessian
327 \& make_edi generates essential-dynamics input file from g_nmeig analysis
328 \& g_anaeig analyzes the normal modes
329 \& g_nmens generates an ensemble of structures from the normal modes
332 .SH "ADDITIONAL DOCUMENTATION"
333 .IX Header "ADDITIONAL DOCUMENTATION"
334 Consult the manual at <\fIhttp://www.gromacs.org/content/view/27/42/\fR> for an
335 introduction to molecular dynamics in general and GROMACS in particular,
336 as well as an overview of the individual programs.
338 The shorter HTML reference and GROMACS FAQ are available in \fB/usr/share/doc/gromacs/html/\fR .
340 Tutorial files and other miscellaneous references are stored in \fB/usr/share/gromacs/\fR .
342 .IX Header "REFERENCES"
343 The development of GROMACS is mainly funded by academic research grants.
344 To help us fund development, the authors humbly ask that you cite the GROMACS papers:
346 H.J.C. Berendsen, D. van der Spoel and R. van Drunen. \fBGROMACS: A message-passing
347 parallel molecular dynamics implementation\fR. Comp. Phys. Comm. \fI91\fR, 43-56 (1995)
349 Erik Lindahl, Berk Hess and David van der Spoel. \fBGROMACS 3.0: A package for
350 molecular simulation and trajectory analysis\fR. J. Mol. Mod. \fI7\fR, 306-317 (2001)
352 B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl. \fBGROMACS 4: Algorithms for
353 Highly Efficient, Load-Balanced, and Scalable Molecular Simulation\fR. J. Chem. Theory
354 Comput. \fI4\fR, 3, 435-447 (2008), <\fIhttp://dx.doi.org/10.1021/ct700301q\fR>
359 David van der Spoel <spoel@gromacs.org>
361 Berk Hess <hess@gromacs.org>
363 Erik Lindahl <lindahl@gromacs.org>
365 A full list of present and former contributors
366 is available at <http://www.gromacs.org>
368 This manual page is largely based on the GROMACS online reference, and was
369 prepared in this format by Nicholas Breen <nbreen@ofb.net>.
372 GROMACS has no major known bugs, but be warned that it stresses your CPU more
373 than most software. Systems with slightly flaky hardware may prove unreliable
374 while running heavy-duty simulations. If at all possible, please try to
375 reproduce bugs on another machine before reporting them.