1GMX(1) GROMACS GMX(1)
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6 gmx - molecular dynamics simulation suite
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9 gmx [-[no]h] [-[no]quiet] [-[no]version] [-[no]copyright] [-nice <int>]
10 [-[no]backup]
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13 GROMACS is a full-featured suite of programs to perform molecular dy‐
14 namics simulations, i.e., to simulate the behavior of systems with hun‐
15 dreds to millions of particles using Newtonian equations of motion. It
16 is primarily used for research on proteins, lipids, and polymers, but
17 can be applied to a wide variety of chemical and biological research
18 questions.
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21 Other options:
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23 -[no]h (no)
24 Print help and quit
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26 -[no]quiet (no)
27 Do not print common startup info or quotes
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29 -[no]version (no)
30 Print extended version information and quit
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32 -[no]copyright (no)
33 Print copyright information on startup
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35 -nice <int> (19)
36 Set the nicelevel (default depends on command)
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38 -[no]backup (yes)
39 Write backups if output files exist
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42 The following commands are available. Please refer to their individual
43 man pages or gmx help <command> for further details.
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45 Trajectory analysis
46 gmx-gangle(1)
47 Calculate angles
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49 gmx-convert-trj(1)
50 Converts between different trajectory types
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52 gmx-distance(1)
53 Calculate distances between pairs of positions
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55 gmx-extract-cluster(1)
56 Allows extracting frames corresponding to clusters from trajec‐
57 tory
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59 gmx-freevolume(1)
60 Calculate free volume
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62 gmx-msd(1)
63 Compute mean squared displacements
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65 gmx-pairdist(1)
66 Calculate pairwise distances between groups of positions
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68 gmx-rdf(1)
69 Calculate radial distribution functions
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71 gmx-sasa(1)
72 Compute solvent accessible surface area
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74 gmx-select(1)
75 Print general information about selections
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77 gmx-trajectory(1)
78 Print coordinates, velocities, and/or forces for selections
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80 Generating topologies and coordinates
81 gmx-editconf(1)
82 Edit the box and write subgroups
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84 gmx-x2top(1)
85 Generate a primitive topology from coordinates
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87 gmx-solvate(1)
88 Solvate a system
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90 gmx-insert-molecules(1)
91 Insert molecules into existing vacancies
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93 gmx-genconf(1)
94 Multiply a conformation in 'random' orientations
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96 gmx-genion(1)
97 Generate monoatomic ions on energetically favorable positions
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99 gmx-genrestr(1)
100 Generate position restraints or distance restraints for index
101 groups
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103 gmx-pdb2gmx(1)
104 Convert coordinate files to topology and FF-compliant coordinate
105 files
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107 Running a simulation
108 gmx-grompp(1)
109 Make a run input file
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111 gmx-mdrun(1)
112 Perform a simulation, do a normal mode analysis or an energy
113 minimization
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115 gmx-convert-tpr(1)
116 Make a modifed run-input file
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118 Viewing trajectories
119 gmx-nmtraj(1)
120 Generate a virtual oscillating trajectory from an eigenvector
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122 gmx-view(1)
123 View a trajectory on an X-Windows terminal
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125 Processing energies
126 gmx-enemat(1)
127 Extract an energy matrix from an energy file
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129 gmx-energy(1)
130 Writes energies to xvg files and display averages
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132 gmx-mdrun(1)
133 (Re)calculate energies for trajectory frames with -rerun
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135 Converting files
136 gmx-editconf(1)
137 Convert and manipulates structure files
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139 gmx-eneconv(1)
140 Convert energy files
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142 gmx-sigeps(1)
143 Convert c6/12 or c6/cn combinations to and from sigma/epsilon
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145 gmx-trjcat(1)
146 Concatenate trajectory files
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148 gmx-trjconv(1)
149 Convert and manipulates trajectory files
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151 gmx-xpm2ps(1)
152 Convert XPM (XPixelMap) matrices to postscript or XPM
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154 Tools
155 gmx-analyze(1)
156 Analyze data sets
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158 gmx-awh(1)
159 Extract data from an accelerated weight histogram (AWH) run
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161 gmx-filter(1)
162 Frequency filter trajectories, useful for making smooth movies
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164 gmx-lie(1)
165 Estimate free energy from linear combinations
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167 gmx-pme_error(1)
168 Estimate the error of using PME with a given input file
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170 gmx-sham(1)
171 Compute free energies or other histograms from histograms
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173 gmx-spatial(1)
174 Calculate the spatial distribution function
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176 gmx-traj(1)
177 Plot x, v, f, box, temperature and rotational energy from tra‐
178 jectories
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180 gmx-tune_pme(1)
181 Time mdrun as a function of PME ranks to optimize settings
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183 gmx-wham(1)
184 Perform weighted histogram analysis after umbrella sampling
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186 gmx-check(1)
187 Check and compare files
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189 gmx-dump(1)
190 Make binary files human readable
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192 gmx-make_ndx(1)
193 Make index files
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195 gmx-mk_angndx(1)
196 Generate index files for 'gmx angle'
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198 gmx-trjorder(1)
199 Order molecules according to their distance to a group
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201 gmx-xpm2ps(1)
202 Convert XPM (XPixelMap) matrices to postscript or XPM
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204 gmx-report-methods(1)
205 Write short summary about the simulation setup to a text file
206 and/or to the standard output.
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208 Distances between structures
209 gmx-cluster(1)
210 Cluster structures
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212 gmx-confrms(1)
213 Fit two structures and calculates the RMSD
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215 gmx-rms(1)
216 Calculate RMSDs with a reference structure and RMSD matrices
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218 gmx-rmsf(1)
219 Calculate atomic fluctuations
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221 Distances in structures over time
222 gmx-mindist(1)
223 Calculate the minimum distance between two groups
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225 gmx-mdmat(1)
226 Calculate residue contact maps
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228 gmx-polystat(1)
229 Calculate static properties of polymers
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231 gmx-rmsdist(1)
232 Calculate atom pair distances averaged with power -2, -3 or -6
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234 Mass distribution properties over time
235 gmx-gyrate(1)
236 Calculate the radius of gyration
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238 gmx-polystat(1)
239 Calculate static properties of polymers
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241 gmx-rdf(1)
242 Calculate radial distribution functions
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244 gmx-rotacf(1)
245 Calculate the rotational correlation function for molecules
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247 gmx-rotmat(1)
248 Plot the rotation matrix for fitting to a reference structure
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250 gmx-sans(1)
251 Compute small angle neutron scattering spectra
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253 gmx-saxs(1)
254 Compute small angle X-ray scattering spectra
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256 gmx-traj(1)
257 Plot x, v, f, box, temperature and rotational energy from tra‐
258 jectories
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260 gmx-vanhove(1)
261 Compute Van Hove displacement and correlation functions
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263 Analyzing bonded interactions
264 gmx-angle(1)
265 Calculate distributions and correlations for angles and dihe‐
266 drals
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268 gmx-mk_angndx(1)
269 Generate index files for 'gmx angle'
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271 Structural properties
272 gmx-bundle(1)
273 Analyze bundles of axes, e.g., helices
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275 gmx-clustsize(1)
276 Calculate size distributions of atomic clusters
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278 gmx-disre(1)
279 Analyze distance restraints
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281 gmx-hbond(1)
282 Compute and analyze hydrogen bonds
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284 gmx-order(1)
285 Compute the order parameter per atom for carbon tails
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287 gmx-principal(1)
288 Calculate principal axes of inertia for a group of atoms
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290 gmx-rdf(1)
291 Calculate radial distribution functions
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293 gmx-saltbr(1)
294 Compute salt bridges
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296 gmx-sorient(1)
297 Analyze solvent orientation around solutes
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299 gmx-spol(1)
300 Analyze solvent dipole orientation and polarization around
301 solutes
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303 Kinetic properties
304 gmx-bar(1)
305 Calculate free energy difference estimates through Bennett's ac‐
306 ceptance ratio
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308 gmx-current(1)
309 Calculate dielectric constants and current autocorrelation func‐
310 tion
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312 gmx-dos(1)
313 Analyze density of states and properties based on that
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315 gmx-dyecoupl(1)
316 Extract dye dynamics from trajectories
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318 gmx-principal(1)
319 Calculate principal axes of inertia for a group of atoms
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321 gmx-tcaf(1)
322 Calculate viscosities of liquids
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324 gmx-traj(1)
325 Plot x, v, f, box, temperature and rotational energy from tra‐
326 jectories
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328 gmx-vanhove(1)
329 Compute Van Hove displacement and correlation functions
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331 gmx-velacc(1)
332 Calculate velocity autocorrelation functions
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334 Electrostatic properties
335 gmx-current(1)
336 Calculate dielectric constants and current autocorrelation func‐
337 tion
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339 gmx-dielectric(1)
340 Calculate frequency dependent dielectric constants
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342 gmx-dipoles(1)
343 Compute the total dipole plus fluctuations
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345 gmx-potential(1)
346 Calculate the electrostatic potential across the box
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348 gmx-spol(1)
349 Analyze solvent dipole orientation and polarization around
350 solutes
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352 gmx-genion(1)
353 Generate monoatomic ions on energetically favorable positions
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355 Protein-specific analysis
356 gmx-do_dssp(1)
357 Assign secondary structure and calculate solvent accessible sur‐
358 face area
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360 gmx-chi(1)
361 Calculate everything you want to know about chi and other dihe‐
362 drals
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364 gmx-helix(1)
365 Calculate basic properties of alpha helices
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367 gmx-helixorient(1)
368 Calculate local pitch/bending/rotation/orientation inside he‐
369 lices
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371 gmx-rama(1)
372 Compute Ramachandran plots
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374 gmx-wheel(1)
375 Plot helical wheels
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377 Interfaces
378 gmx-bundle(1)
379 Analyze bundles of axes, e.g., helices
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381 gmx-density(1)
382 Calculate the density of the system
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384 gmx-densmap(1)
385 Calculate 2D planar or axial-radial density maps
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387 gmx-densorder(1)
388 Calculate surface fluctuations
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390 gmx-h2order(1)
391 Compute the orientation of water molecules
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393 gmx-hydorder(1)
394 Compute tetrahedrality parameters around a given atom
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396 gmx-order(1)
397 Compute the order parameter per atom for carbon tails
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399 gmx-potential(1)
400 Calculate the electrostatic potential across the box
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402 Covariance analysis
403 gmx-anaeig(1)
404 Analyze the eigenvectors
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406 gmx-covar(1)
407 Calculate and diagonalize the covariance matrix
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409 gmx-make_edi(1)
410 Generate input files for essential dynamics sampling
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412 Normal modes
413 gmx-anaeig(1)
414 Analyze the normal modes
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416 gmx-nmeig(1)
417 Diagonalize the Hessian for normal mode analysis
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419 gmx-nmtraj(1)
420 Generate a virtual oscillating trajectory from an eigenvector
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422 gmx-nmens(1)
423 Generate an ensemble of structures from the normal modes
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425 gmx-grompp(1)
426 Make a run input file
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428 gmx-mdrun(1)
429 Find a potential energy minimum and calculate the Hessian
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432 2022, GROMACS development team
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4372022.3 Sep 02, 2022 GMX(1)