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
14 dynamics simulations, i.e., to simulate the behavior of systems with
15 hundreds to millions of particles using Newtonian equations of motion.
16 It is primarily used for research on proteins, lipids, and polymers,
17 but can be applied to a wide variety of chemical and biological
18 research 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 (yes)
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
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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.
44 Trajectory analysis
46 gmx-gangle(1)
47 Calculate angles
48 gmx-distance(1)
50 Calculate distances between pairs of positions
51 gmx-freevolume(1)
53 Calculate free volume
54 gmx-pairdist(1)
56 Calculate pairwise distances between groups of positions
57 gmx-rdf(1)
59 Calculate radial distribution functions
60 gmx-sasa(1)
62 Compute solvent accessible surface area
63 gmx-select(1)
65 Print general information about selections
66 gmx-trajectory(1)
68 Print coordinates, velocities, and/or forces for selections
69 Generating topologies and coordinates
71 gmx-editconf(1)
72 Edit the box and write subgroups
73 gmx-x2top(1)
75 Generate a primitive topology from coordinates
76 gmx-solvate(1)
78 Solvate a system
79 gmx-insert-molecules(1)
81 Insert molecules into existing vacancies
82 gmx-genconf(1)
84 Multiply a conformation in ‘random’ orientations
85 gmx-genion(1)
87 Generate monoatomic ions on energetically favorable positions
88 gmx-genrestr(1)
90 Generate position restraints or distance restraints for index
91 groups
92 gmx-pdb2gmx(1)
94 Convert coordinate files to topology and FF-compliant coordinate
95 files
96 Running a simulation
98 gmx-grompp(1)
99 Make a run input file
100 gmx-mdrun(1)
102 Perform a simulation, do a normal mode analysis or an energy
103 minimization
104 gmx-convert-tpr(1)
106 Make a modifed run-input file
107 Viewing trajectories
109 gmx-nmtraj(1)
110 Generate a virtual oscillating trajectory from an eigenvector
111 gmx-view(1)
113 View a trajectory on an X-Windows terminal
114 Processing energies
116 gmx-enemat(1)
117 Extract an energy matrix from an energy file
118 gmx-energy(1)
120 Writes energies to xvg files and display averages
121 gmx-mdrun(1)
123 (Re)calculate energies for trajectory frames with -rerun
124 Converting files
126 gmx-editconf(1)
127 Convert and manipulates structure files
128 gmx-eneconv(1)
130 Convert energy files
131 gmx-sigeps(1)
133 Convert c6/12 or c6/cn combinations to and from sigma/epsilon
134 gmx-trjcat(1)
136 Concatenate trajectory files
137 gmx-trjconv(1)
139 Convert and manipulates trajectory files
140 gmx-xpm2ps(1)
142 Convert XPM (XPixelMap) matrices to postscript or XPM
143 Tools
145 gmx-analyze(1)
146 Analyze data sets
147 gmx-awh(1)
149 Extract data from an accelerated weight histogram (AWH) run
150 gmx-dyndom(1)
152 Interpolate and extrapolate structure rotations
153 gmx-filter(1)
155 Frequency filter trajectories, useful for making smooth movies
156 gmx-lie(1)
158 Estimate free energy from linear combinations
159 gmx-morph(1)
161 Interpolate linearly between conformations
162 gmx-pme_error(1)
164 Estimate the error of using PME with a given input file
165 gmx-sham(1)
167 Compute free energies or other histograms from histograms
168 gmx-spatial(1)
170 Calculate the spatial distribution function
171 gmx-traj(1)
173 Plot x, v, f, box, temperature and rotational energy from tra‐
174 jectories
175 gmx-tune_pme(1)
177 Time mdrun as a function of PME ranks to optimize settings
178 gmx-wham(1)
180 Perform weighted histogram analysis after umbrella sampling
181 gmx-check(1)
183 Check and compare files
184 gmx-dump(1)
186 Make binary files human readable
187 gmx-make_ndx(1)
189 Make index files
190 gmx-mk_angndx(1)
192 Generate index files for ‘gmx angle’
193 gmx-trjorder(1)
195 Order molecules according to their distance to a group
196 gmx-xpm2ps(1)
198 Convert XPM (XPixelMap) matrices to postscript or XPM
199 gmx-report-methods(1)
201 Write short summary about the simulation setup to a text file
202 and/or to the standard output.
203 Distances between structures
205 gmx-cluster(1)
206 Cluster structures
207 gmx-confrms(1)
209 Fit two structures and calculates the RMSD
210 gmx-rms(1)
212 Calculate RMSDs with a reference structure and RMSD matrices
213 gmx-rmsf(1)
215 Calculate atomic fluctuations
216 Distances in structures over time
218 gmx-mindist(1)
219 Calculate the minimum distance between two groups
220 gmx-mdmat(1)
222 Calculate residue contact maps
223 gmx-polystat(1)
225 Calculate static properties of polymers
226 gmx-rmsdist(1)
228 Calculate atom pair distances averaged with power -2, -3 or -6
229 Mass distribution properties over time
231 gmx-gyrate(1)
232 Calculate the radius of gyration
233 gmx-msd(1)
235 Calculates mean square displacements
236 gmx-polystat(1)
238 Calculate static properties of polymers
239 gmx-rdf(1)
241 Calculate radial distribution functions
242 gmx-rotacf(1)
244 Calculate the rotational correlation function for molecules
245 gmx-rotmat(1)
247 Plot the rotation matrix for fitting to a reference structure
248 gmx-sans(1)
250 Compute small angle neutron scattering spectra
251 gmx-saxs(1)
253 Compute small angle X-ray scattering spectra
254 gmx-traj(1)
256 Plot x, v, f, box, temperature and rotational energy from tra‐
257 jectories
258 gmx-vanhove(1)
260 Compute Van Hove displacement and correlation functions
261 Analyzing bonded interactions
263 gmx-angle(1)
264 Calculate distributions and correlations for angles and dihe‐
265 drals
266 gmx-mk_angndx(1)
268 Generate index files for ‘gmx angle’
269 Structural properties
271 gmx-anadock(1)
272 Cluster structures from Autodock runs
273 gmx-bundle(1)
275 Analyze bundles of axes, e.g., helices
276 gmx-clustsize(1)
278 Calculate size distributions of atomic clusters
279 gmx-disre(1)
281 Analyze distance restraints
282 gmx-hbond(1)
284 Compute and analyze hydrogen bonds
285 gmx-order(1)
287 Compute the order parameter per atom for carbon tails
288 gmx-principal(1)
290 Calculate principal axes of inertia for a group of atoms
291 gmx-rdf(1)
293 Calculate radial distribution functions
294 gmx-saltbr(1)
296 Compute salt bridges
297 gmx-sorient(1)
299 Analyze solvent orientation around solutes
300 gmx-spol(1)
302 Analyze solvent dipole orientation and polarization around
303 solutes
304 Kinetic properties
306 gmx-bar(1)
307 Calculate free energy difference estimates through Bennett’s
308 acceptance ratio
309 gmx-current(1)
311 Calculate dielectric constants and current autocorrelation func‐
312 tion
313 gmx-dos(1)
315 Analyze density of states and properties based on that
316 gmx-dyecoupl(1)
318 Extract dye dynamics from trajectories
319 gmx-principal(1)
321 Calculate principal axes of inertia for a group of atoms
322 gmx-tcaf(1)
324 Calculate viscosities of liquids
325 gmx-traj(1)
327 Plot x, v, f, box, temperature and rotational energy from tra‐
328 jectories
329 gmx-vanhove(1)
331 Compute Van Hove displacement and correlation functions
332 gmx-velacc(1)
334 Calculate velocity autocorrelation functions
335 Electrostatic properties
337 gmx-current(1)
338 Calculate dielectric constants and current autocorrelation func‐
339 tion
340 gmx-dielectric(1)
342 Calculate frequency dependent dielectric constants
343 gmx-dipoles(1)
345 Compute the total dipole plus fluctuations
346 gmx-potential(1)
348 Calculate the electrostatic potential across the box
349 gmx-spol(1)
351 Analyze solvent dipole orientation and polarization around
352 solutes
353 gmx-genion(1)
355 Generate monoatomic ions on energetically favorable positions
356 Protein-specific analysis
358 gmx-do_dssp(1)
359 Assign secondary structure and calculate solvent accessible sur‐
360 face area
361 gmx-chi(1)
363 Calculate everything you want to know about chi and other dihe‐
364 drals
365 gmx-helix(1)
367 Calculate basic properties of alpha helices
368 gmx-helixorient(1)
370 Calculate local pitch/bending/rotation/orientation inside
371 helices
372 gmx-rama(1)
374 Compute Ramachandran plots
375 gmx-wheel(1)
377 Plot helical wheels
378 Interfaces
380 gmx-bundle(1)
381 Analyze bundles of axes, e.g., helices
382 gmx-density(1)
384 Calculate the density of the system
385 gmx-densmap(1)
387 Calculate 2D planar or axial-radial density maps
388 gmx-densorder(1)
390 Calculate surface fluctuations
391 gmx-h2order(1)
393 Compute the orientation of water molecules
394 gmx-hydorder(1)
396 Compute tetrahedrality parameters around a given atom
397 gmx-order(1)
399 Compute the order parameter per atom for carbon tails
400 gmx-potential(1)
402 Calculate the electrostatic potential across the box
403 Covariance analysis
405 gmx-anaeig(1)
406 Analyze the eigenvectors
407 gmx-covar(1)
409 Calculate and diagonalize the covariance matrix
410 gmx-make_edi(1)
412 Generate input files for essential dynamics sampling
413 Normal modes
415 gmx-anaeig(1)
416 Analyze the normal modes
417 gmx-nmeig(1)
419 Diagonalize the Hessian for normal mode analysis
420 gmx-nmtraj(1)
422 Generate a virtual oscillating trajectory from an eigenvector
423 gmx-nmens(1)
425 Generate an ensemble of structures from the normal modes
426 gmx-grompp(1)
428 Make a run input file
429 gmx-mdrun(1)
431 Find a potential energy minimum and calculate the Hessian
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434 2020, GROMACS development team
4352019.6 Feb 28, 2020 GMX(1)