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:
22 -[no]h (no)
24 Print help and quit
25 -[no]quiet (no)
27 Do not print common startup info or quotes
28 -[no]version (no)
30 Print extended version information and quit
31 -[no]copyright (no)
33 Print copyright information on startup
34 -nice <int> (19)
36 Set the nicelevel (default depends on command)
37 -[no]backup (yes)
39 Write backups if output files exist
40
42 The following commands are available. Please refer to their individual
43 man pages or gmx help <command> for further details.
44 Trajectory analysis
46 gmx-gangle(1)
47 Calculate angles
48 gmx-convert-trj(1)
50 Converts between different trajectory types
51 gmx-distance(1)
53 Calculate distances between pairs of positions
54 gmx-extract-cluster(1)
56 Allows extracting frames corresponding to clusters from trajec‐
57 tory
58 gmx-freevolume(1)
60 Calculate free volume
61 gmx-msd(1)
63 Compute mean squared displacements
64 gmx-pairdist(1)
66 Calculate pairwise distances between groups of positions
67 gmx-rdf(1)
69 Calculate radial distribution functions
70 gmx-sasa(1)
72 Compute solvent accessible surface area
73 gmx-select(1)
75 Print general information about selections
76 gmx-trajectory(1)
78 Print coordinates, velocities, and/or forces for selections
79 Generating topologies and coordinates
81 gmx-editconf(1)
82 Edit the box and write subgroups
83 gmx-x2top(1)
85 Generate a primitive topology from coordinates
86 gmx-solvate(1)
88 Solvate a system
89 gmx-insert-molecules(1)
91 Insert molecules into existing vacancies
92 gmx-genconf(1)
94 Multiply a conformation in 'random' orientations
95 gmx-genion(1)
97 Generate monoatomic ions on energetically favorable positions
98 gmx-genrestr(1)
100 Generate position restraints or distance restraints for index
101 groups
102 gmx-pdb2gmx(1)
104 Convert coordinate files to topology and FF-compliant coordinate
105 files
106 Running a simulation
108 gmx-grompp(1)
109 Make a run input file
110 gmx-mdrun(1)
112 Perform a simulation, do a normal mode analysis or an energy
113 minimization
114 gmx-convert-tpr(1)
116 Make a modifed run-input file
117 Viewing trajectories
119 gmx-nmtraj(1)
120 Generate a virtual oscillating trajectory from an eigenvector
121 gmx-view(1)
123 View a trajectory on an X-Windows terminal
124 Processing energies
126 gmx-enemat(1)
127 Extract an energy matrix from an energy file
128 gmx-energy(1)
130 Writes energies to xvg files and display averages
131 gmx-mdrun(1)
133 (Re)calculate energies for trajectory frames with -rerun
134 Converting files
136 gmx-editconf(1)
137 Convert and manipulates structure files
138 gmx-eneconv(1)
140 Convert energy files
141 gmx-sigeps(1)
143 Convert c6/12 or c6/cn combinations to and from sigma/epsilon
144 gmx-trjcat(1)
146 Concatenate trajectory files
147 gmx-trjconv(1)
149 Convert and manipulates trajectory files
150 gmx-xpm2ps(1)
152 Convert XPM (XPixelMap) matrices to postscript or XPM
153 Tools
155 gmx-analyze(1)
156 Analyze data sets
157 gmx-awh(1)
159 Extract data from an accelerated weight histogram (AWH) run
160 gmx-filter(1)
162 Frequency filter trajectories, useful for making smooth movies
163 gmx-lie(1)
165 Estimate free energy from linear combinations
166 gmx-pme_error(1)
168 Estimate the error of using PME with a given input file
169 gmx-sham(1)
171 Compute free energies or other histograms from histograms
172 gmx-spatial(1)
174 Calculate the spatial distribution function
175 gmx-traj(1)
177 Plot x, v, f, box, temperature and rotational energy from tra‐
178 jectories
179 gmx-tune_pme(1)
181 Time mdrun as a function of PME ranks to optimize settings
182 gmx-wham(1)
184 Perform weighted histogram analysis after umbrella sampling
185 gmx-check(1)
187 Check and compare files
188 gmx-dump(1)
190 Make binary files human readable
191 gmx-make_ndx(1)
193 Make index files
194 gmx-mk_angndx(1)
196 Generate index files for 'gmx angle'
197 gmx-trjorder(1)
199 Order molecules according to their distance to a group
200 gmx-xpm2ps(1)
202 Convert XPM (XPixelMap) matrices to postscript or XPM
203 gmx-report-methods(1)
205 Write short summary about the simulation setup to a text file
206 and/or to the standard output.
207 Distances between structures
209 gmx-cluster(1)
210 Cluster structures
211 gmx-confrms(1)
213 Fit two structures and calculates the RMSD
214 gmx-rms(1)
216 Calculate RMSDs with a reference structure and RMSD matrices
217 gmx-rmsf(1)
219 Calculate atomic fluctuations
220 Distances in structures over time
222 gmx-mindist(1)
223 Calculate the minimum distance between two groups
224 gmx-mdmat(1)
226 Calculate residue contact maps
227 gmx-polystat(1)
229 Calculate static properties of polymers
230 gmx-rmsdist(1)
232 Calculate atom pair distances averaged with power -2, -3 or -6
233 Mass distribution properties over time
235 gmx-gyrate(1)
236 Calculate the radius of gyration
237 gmx-polystat(1)
239 Calculate static properties of polymers
240 gmx-rdf(1)
242 Calculate radial distribution functions
243 gmx-rotacf(1)
245 Calculate the rotational correlation function for molecules
246 gmx-rotmat(1)
248 Plot the rotation matrix for fitting to a reference structure
249 gmx-sans(1)
251 Compute small angle neutron scattering spectra
252 gmx-saxs(1)
254 Compute small angle X-ray scattering spectra
255 gmx-traj(1)
257 Plot x, v, f, box, temperature and rotational energy from tra‐
258 jectories
259 gmx-vanhove(1)
261 Compute Van Hove displacement and correlation functions
262 Analyzing bonded interactions
264 gmx-angle(1)
265 Calculate distributions and correlations for angles and dihe‐
266 drals
267 gmx-mk_angndx(1)
269 Generate index files for 'gmx angle'
270 Structural properties
272 gmx-bundle(1)
273 Analyze bundles of axes, e.g., helices
274 gmx-clustsize(1)
276 Calculate size distributions of atomic clusters
277 gmx-disre(1)
279 Analyze distance restraints
280 gmx-hbond(1)
282 Compute and analyze hydrogen bonds
283 gmx-order(1)
285 Compute the order parameter per atom for carbon tails
286 gmx-principal(1)
288 Calculate principal axes of inertia for a group of atoms
289 gmx-rdf(1)
291 Calculate radial distribution functions
292 gmx-saltbr(1)
294 Compute salt bridges
295 gmx-sorient(1)
297 Analyze solvent orientation around solutes
298 gmx-spol(1)
300 Analyze solvent dipole orientation and polarization around
301 solutes
302 Kinetic properties
304 gmx-bar(1)
305 Calculate free energy difference estimates through Bennett's ac‐
306 ceptance ratio
307 gmx-current(1)
309 Calculate dielectric constants and current autocorrelation func‐
310 tion
311 gmx-dos(1)
313 Analyze density of states and properties based on that
314 gmx-dyecoupl(1)
316 Extract dye dynamics from trajectories
317 gmx-principal(1)
319 Calculate principal axes of inertia for a group of atoms
320 gmx-tcaf(1)
322 Calculate viscosities of liquids
323 gmx-traj(1)
325 Plot x, v, f, box, temperature and rotational energy from tra‐
326 jectories
327 gmx-vanhove(1)
329 Compute Van Hove displacement and correlation functions
330 gmx-velacc(1)
332 Calculate velocity autocorrelation functions
333 Electrostatic properties
335 gmx-current(1)
336 Calculate dielectric constants and current autocorrelation func‐
337 tion
338 gmx-dielectric(1)
340 Calculate frequency dependent dielectric constants
341 gmx-dipoles(1)
343 Compute the total dipole plus fluctuations
344 gmx-potential(1)
346 Calculate the electrostatic potential across the box
347 gmx-spol(1)
349 Analyze solvent dipole orientation and polarization around
350 solutes
351 gmx-genion(1)
353 Generate monoatomic ions on energetically favorable positions
354 Protein-specific analysis
356 gmx-do_dssp(1)
357 Assign secondary structure and calculate solvent accessible sur‐
358 face area
359 gmx-chi(1)
361 Calculate everything you want to know about chi and other dihe‐
362 drals
363 gmx-helix(1)
365 Calculate basic properties of alpha helices
366 gmx-helixorient(1)
368 Calculate local pitch/bending/rotation/orientation inside he‐
369 lices
370 gmx-rama(1)
372 Compute Ramachandran plots
373 gmx-wheel(1)
375 Plot helical wheels
376 Interfaces
378 gmx-bundle(1)
379 Analyze bundles of axes, e.g., helices
380 gmx-density(1)
382 Calculate the density of the system
383 gmx-densmap(1)
385 Calculate 2D planar or axial-radial density maps
386 gmx-densorder(1)
388 Calculate surface fluctuations
389 gmx-h2order(1)
391 Compute the orientation of water molecules
392 gmx-hydorder(1)
394 Compute tetrahedrality parameters around a given atom
395 gmx-order(1)
397 Compute the order parameter per atom for carbon tails
398 gmx-potential(1)
400 Calculate the electrostatic potential across the box
401 Covariance analysis
403 gmx-anaeig(1)
404 Analyze the eigenvectors
405 gmx-covar(1)
407 Calculate and diagonalize the covariance matrix
408 gmx-make_edi(1)
410 Generate input files for essential dynamics sampling
411 Normal modes
413 gmx-anaeig(1)
414 Analyze the normal modes
415 gmx-nmeig(1)
417 Diagonalize the Hessian for normal mode analysis
418 gmx-nmtraj(1)
420 Generate a virtual oscillating trajectory from an eigenvector
421 gmx-nmens(1)
423 Generate an ensemble of structures from the normal modes
424 gmx-grompp(1)
426 Make a run input file
427 gmx-mdrun(1)
429 Find a potential energy minimum and calculate the Hessian
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432 2022, GROMACS development team
4332022.3 Sep 02, 2022 GMX(1)