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 Distances between structures
201 gmx-cluster(1)
202 Cluster structures
203 gmx-confrms(1)
205 Fit two structures and calculates the RMSD
206 gmx-rms(1)
208 Calculate RMSDs with a reference structure and RMSD matrices
209 gmx-rmsf(1)
211 Calculate atomic fluctuations
212 Distances in structures over time
214 gmx-mindist(1)
215 Calculate the minimum distance between two groups
216 gmx-mdmat(1)
218 Calculate residue contact maps
219 gmx-polystat(1)
221 Calculate static properties of polymers
222 gmx-rmsdist(1)
224 Calculate atom pair distances averaged with power -2, -3 or -6
225 Mass distribution properties over time
227 gmx-gyrate(1)
228 Calculate the radius of gyration
229 gmx-msd(1)
231 Calculates mean square displacements
232 gmx-polystat(1)
234 Calculate static properties of polymers
235 gmx-rdf(1)
237 Calculate radial distribution functions
238 gmx-rotacf(1)
240 Calculate the rotational correlation function for molecules
241 gmx-rotmat(1)
243 Plot the rotation matrix for fitting to a reference structure
244 gmx-sans(1)
246 Compute small angle neutron scattering spectra
247 gmx-saxs(1)
249 Compute small angle X-ray scattering spectra
250 gmx-traj(1)
252 Plot x, v, f, box, temperature and rotational energy from tra‐
253 jectories
254 gmx-vanhove(1)
256 Compute Van Hove displacement and correlation functions
257 Analyzing bonded interactions
259 gmx-angle(1)
260 Calculate distributions and correlations for angles and dihe‐
261 drals
262 gmx-mk_angndx(1)
264 Generate index files for ‘gmx angle’
265 Structural properties
267 gmx-anadock(1)
268 Cluster structures from Autodock runs
269 gmx-bundle(1)
271 Analyze bundles of axes, e.g., helices
272 gmx-clustsize(1)
274 Calculate size distributions of atomic clusters
275 gmx-disre(1)
277 Analyze distance restraints
278 gmx-hbond(1)
280 Compute and analyze hydrogen bonds
281 gmx-order(1)
283 Compute the order parameter per atom for carbon tails
284 gmx-principal(1)
286 Calculate principal axes of inertia for a group of atoms
287 gmx-rdf(1)
289 Calculate radial distribution functions
290 gmx-saltbr(1)
292 Compute salt bridges
293 gmx-sorient(1)
295 Analyze solvent orientation around solutes
296 gmx-spol(1)
298 Analyze solvent dipole orientation and polarization around
299 solutes
300 Kinetic properties
302 gmx-bar(1)
303 Calculate free energy difference estimates through Bennett’s
304 acceptance ratio
305 gmx-current(1)
307 Calculate dielectric constants and current autocorrelation func‐
308 tion
309 gmx-dos(1)
311 Analyze density of states and properties based on that
312 gmx-dyecoupl(1)
314 Extract dye dynamics from trajectories
315 gmx-principal(1)
317 Calculate principal axes of inertia for a group of atoms
318 gmx-tcaf(1)
320 Calculate viscosities of liquids
321 gmx-traj(1)
323 Plot x, v, f, box, temperature and rotational energy from tra‐
324 jectories
325 gmx-vanhove(1)
327 Compute Van Hove displacement and correlation functions
328 gmx-velacc(1)
330 Calculate velocity autocorrelation functions
331 Electrostatic properties
333 gmx-current(1)
334 Calculate dielectric constants and current autocorrelation func‐
335 tion
336 gmx-dielectric(1)
338 Calculate frequency dependent dielectric constants
339 gmx-dipoles(1)
341 Compute the total dipole plus fluctuations
342 gmx-potential(1)
344 Calculate the electrostatic potential across the box
345 gmx-spol(1)
347 Analyze solvent dipole orientation and polarization around
348 solutes
349 gmx-genion(1)
351 Generate monoatomic ions on energetically favorable positions
352 Protein-specific analysis
354 gmx-do_dssp(1)
355 Assign secondary structure and calculate solvent accessible sur‐
356 face area
357 gmx-chi(1)
359 Calculate everything you want to know about chi and other dihe‐
360 drals
361 gmx-helix(1)
363 Calculate basic properties of alpha helices
364 gmx-helixorient(1)
366 Calculate local pitch/bending/rotation/orientation inside
367 helices
368 gmx-rama(1)
370 Compute Ramachandran plots
371 gmx-wheel(1)
373 Plot helical wheels
374 Interfaces
376 gmx-bundle(1)
377 Analyze bundles of axes, e.g., helices
378 gmx-density(1)
380 Calculate the density of the system
381 gmx-densmap(1)
383 Calculate 2D planar or axial-radial density maps
384 gmx-densorder(1)
386 Calculate surface fluctuations
387 gmx-h2order(1)
389 Compute the orientation of water molecules
390 gmx-hydorder(1)
392 Compute tetrahedrality parameters around a given atom
393 gmx-order(1)
395 Compute the order parameter per atom for carbon tails
396 gmx-potential(1)
398 Calculate the electrostatic potential across the box
399 Covariance analysis
401 gmx-anaeig(1)
402 Analyze the eigenvectors
403 gmx-covar(1)
405 Calculate and diagonalize the covariance matrix
406 gmx-make_edi(1)
408 Generate input files for essential dynamics sampling
409 Normal modes
411 gmx-anaeig(1)
412 Analyze the normal modes
413 gmx-nmeig(1)
415 Diagonalize the Hessian for normal mode analysis
416 gmx-nmtraj(1)
418 Generate a virtual oscillating trajectory from an eigenvector
419 gmx-nmens(1)
421 Generate an ensemble of structures from the normal modes
422 gmx-grompp(1)
424 Make a run input file
425 gmx-mdrun(1)
427 Find a potential energy minimum and calculate the Hessian
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430 2019, GROMACS development team
4312018.7 May 29, 2019 GMX(1)