1GMX(1)                              GROMACS                             GMX(1)
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NAME

6       gmx - molecular dynamics simulation suite
7

SYNOPSIS

9          gmx [-[no]h] [-[no]quiet] [-[no]version] [-[no]copyright] [-nice <int>]
10              [-[no]backup]
11

DESCRIPTION

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.
19

OPTIONS

21       Other options:
22
23       -[no]h (no)
24              Print help and quit
25
26       -[no]quiet (no)
27              Do not print common startup info or quotes
28
29       -[no]version (no)
30              Print extended version information and quit
31
32       -[no]copyright (yes)
33              Print copyright information on startup
34
35       -nice <int> (19)
36              Set the nicelevel (default depends on command)
37
38       -[no]backup (yes)
39              Write backups if output files exist
40

GMX COMMANDS

42       The following commands are available. Please refer to their  individual
43       man pages or gmx help <command> for further details.
44
45   Trajectory analysis
46       gmx-gangle(1)
47              Calculate angles
48
49       gmx-distance(1)
50              Calculate distances between pairs of positions
51
52       gmx-freevolume(1)
53              Calculate free volume
54
55       gmx-pairdist(1)
56              Calculate pairwise distances between groups of positions
57
58       gmx-rdf(1)
59              Calculate radial distribution functions
60
61       gmx-sasa(1)
62              Compute solvent accessible surface area
63
64       gmx-select(1)
65              Print general information about selections
66
67       gmx-trajectory(1)
68              Print coordinates, velocities, and/or forces for selections
69
70   Generating topologies and coordinates
71       gmx-editconf(1)
72              Edit the box and write subgroups
73
74       gmx-x2top(1)
75              Generate a primitive topology from coordinates
76
77       gmx-solvate(1)
78              Solvate a system
79
80       gmx-insert-molecules(1)
81              Insert molecules into existing vacancies
82
83       gmx-genconf(1)
84              Multiply a conformation in ‘random’ orientations
85
86       gmx-genion(1)
87              Generate monoatomic ions on energetically favorable positions
88
89       gmx-genrestr(1)
90              Generate  position  restraints  or distance restraints for index
91              groups
92
93       gmx-pdb2gmx(1)
94              Convert coordinate files to topology and FF-compliant coordinate
95              files
96
97   Running a simulation
98       gmx-grompp(1)
99              Make a run input file
100
101       gmx-mdrun(1)
102              Perform  a  simulation,  do  a normal mode analysis or an energy
103              minimization
104
105       gmx-convert-tpr(1)
106              Make a modifed run-input file
107
108   Viewing trajectories
109       gmx-nmtraj(1)
110              Generate a virtual oscillating trajectory from an eigenvector
111
112       gmx-view(1)
113              View a trajectory on an X-Windows terminal
114
115   Processing energies
116       gmx-enemat(1)
117              Extract an energy matrix from an energy file
118
119       gmx-energy(1)
120              Writes energies to xvg files and display averages
121
122       gmx-mdrun(1)
123              (Re)calculate energies for trajectory frames with -rerun
124
125   Converting files
126       gmx-editconf(1)
127              Convert and manipulates structure files
128
129       gmx-eneconv(1)
130              Convert energy files
131
132       gmx-sigeps(1)
133              Convert c6/12 or c6/cn combinations to and from sigma/epsilon
134
135       gmx-trjcat(1)
136              Concatenate trajectory files
137
138       gmx-trjconv(1)
139              Convert and manipulates trajectory files
140
141       gmx-xpm2ps(1)
142              Convert XPM (XPixelMap) matrices to postscript or XPM
143
144   Tools
145       gmx-analyze(1)
146              Analyze data sets
147
148       gmx-awh(1)
149              Extract data from an accelerated weight histogram (AWH) run
150
151       gmx-dyndom(1)
152              Interpolate and extrapolate structure rotations
153
154       gmx-filter(1)
155              Frequency filter trajectories, useful for making smooth movies
156
157       gmx-lie(1)
158              Estimate free energy from linear combinations
159
160       gmx-morph(1)
161              Interpolate linearly between conformations
162
163       gmx-pme_error(1)
164              Estimate the error of using PME with a given input file
165
166       gmx-sham(1)
167              Compute free energies or other histograms from histograms
168
169       gmx-spatial(1)
170              Calculate the spatial distribution function
171
172       gmx-traj(1)
173              Plot x, v, f, box, temperature and rotational energy  from  tra‐
174              jectories
175
176       gmx-tune_pme(1)
177              Time mdrun as a function of PME ranks to optimize settings
178
179       gmx-wham(1)
180              Perform weighted histogram analysis after umbrella sampling
181
182       gmx-check(1)
183              Check and compare files
184
185       gmx-dump(1)
186              Make binary files human readable
187
188       gmx-make_ndx(1)
189              Make index files
190
191       gmx-mk_angndx(1)
192              Generate index files for ‘gmx angle’
193
194       gmx-trjorder(1)
195              Order molecules according to their distance to a group
196
197       gmx-xpm2ps(1)
198              Convert XPM (XPixelMap) matrices to postscript or XPM
199
200       gmx-report-methods(1)
201              Write  short  summary  about the simulation setup to a text file
202              and/or to the standard output.
203
204   Distances between structures
205       gmx-cluster(1)
206              Cluster structures
207
208       gmx-confrms(1)
209              Fit two structures and calculates the RMSD
210
211       gmx-rms(1)
212              Calculate RMSDs with a reference structure and RMSD matrices
213
214       gmx-rmsf(1)
215              Calculate atomic fluctuations
216
217   Distances in structures over time
218       gmx-mindist(1)
219              Calculate the minimum distance between two groups
220
221       gmx-mdmat(1)
222              Calculate residue contact maps
223
224       gmx-polystat(1)
225              Calculate static properties of polymers
226
227       gmx-rmsdist(1)
228              Calculate atom pair distances averaged with power -2, -3 or -6
229
230   Mass distribution properties over time
231       gmx-gyrate(1)
232              Calculate the radius of gyration
233
234       gmx-msd(1)
235              Calculates mean square displacements
236
237       gmx-polystat(1)
238              Calculate static properties of polymers
239
240       gmx-rdf(1)
241              Calculate radial distribution functions
242
243       gmx-rotacf(1)
244              Calculate the rotational correlation function for molecules
245
246       gmx-rotmat(1)
247              Plot the rotation matrix for fitting to a reference structure
248
249       gmx-sans(1)
250              Compute small angle neutron scattering spectra
251
252       gmx-saxs(1)
253              Compute small angle X-ray scattering spectra
254
255       gmx-traj(1)
256              Plot x, v, f, box, temperature and rotational energy  from  tra‐
257              jectories
258
259       gmx-vanhove(1)
260              Compute Van Hove displacement and correlation functions
261
262   Analyzing bonded interactions
263       gmx-angle(1)
264              Calculate  distributions  and  correlations for angles and dihe‐
265              drals
266
267       gmx-mk_angndx(1)
268              Generate index files for ‘gmx angle’
269
270   Structural properties
271       gmx-anadock(1)
272              Cluster structures from Autodock runs
273
274       gmx-bundle(1)
275              Analyze bundles of axes, e.g., helices
276
277       gmx-clustsize(1)
278              Calculate size distributions of atomic clusters
279
280       gmx-disre(1)
281              Analyze distance restraints
282
283       gmx-hbond(1)
284              Compute and analyze hydrogen bonds
285
286       gmx-order(1)
287              Compute the order parameter per atom for carbon tails
288
289       gmx-principal(1)
290              Calculate principal axes of inertia for a group of atoms
291
292       gmx-rdf(1)
293              Calculate radial distribution functions
294
295       gmx-saltbr(1)
296              Compute salt bridges
297
298       gmx-sorient(1)
299              Analyze solvent orientation around solutes
300
301       gmx-spol(1)
302              Analyze  solvent  dipole  orientation  and  polarization  around
303              solutes
304
305   Kinetic properties
306       gmx-bar(1)
307              Calculate  free  energy  difference  estimates through Bennett’s
308              acceptance ratio
309
310       gmx-current(1)
311              Calculate dielectric constants and current autocorrelation func‐
312              tion
313
314       gmx-dos(1)
315              Analyze density of states and properties based on that
316
317       gmx-dyecoupl(1)
318              Extract dye dynamics from trajectories
319
320       gmx-principal(1)
321              Calculate principal axes of inertia for a group of atoms
322
323       gmx-tcaf(1)
324              Calculate viscosities of liquids
325
326       gmx-traj(1)
327              Plot  x,  v, f, box, temperature and rotational energy from tra‐
328              jectories
329
330       gmx-vanhove(1)
331              Compute Van Hove displacement and correlation functions
332
333       gmx-velacc(1)
334              Calculate velocity autocorrelation functions
335
336   Electrostatic properties
337       gmx-current(1)
338              Calculate dielectric constants and current autocorrelation func‐
339              tion
340
341       gmx-dielectric(1)
342              Calculate frequency dependent dielectric constants
343
344       gmx-dipoles(1)
345              Compute the total dipole plus fluctuations
346
347       gmx-potential(1)
348              Calculate the electrostatic potential across the box
349
350       gmx-spol(1)
351              Analyze  solvent  dipole  orientation  and  polarization  around
352              solutes
353
354       gmx-genion(1)
355              Generate monoatomic ions on energetically favorable positions
356
357   Protein-specific analysis
358       gmx-do_dssp(1)
359              Assign secondary structure and calculate solvent accessible sur‐
360              face area
361
362       gmx-chi(1)
363              Calculate  everything you want to know about chi and other dihe‐
364              drals
365
366       gmx-helix(1)
367              Calculate basic properties of alpha helices
368
369       gmx-helixorient(1)
370              Calculate   local   pitch/bending/rotation/orientation    inside
371              helices
372
373       gmx-rama(1)
374              Compute Ramachandran plots
375
376       gmx-wheel(1)
377              Plot helical wheels
378
379   Interfaces
380       gmx-bundle(1)
381              Analyze bundles of axes, e.g., helices
382
383       gmx-density(1)
384              Calculate the density of the system
385
386       gmx-densmap(1)
387              Calculate 2D planar or axial-radial density maps
388
389       gmx-densorder(1)
390              Calculate surface fluctuations
391
392       gmx-h2order(1)
393              Compute the orientation of water molecules
394
395       gmx-hydorder(1)
396              Compute tetrahedrality parameters around a given atom
397
398       gmx-order(1)
399              Compute the order parameter per atom for carbon tails
400
401       gmx-potential(1)
402              Calculate the electrostatic potential across the box
403
404   Covariance analysis
405       gmx-anaeig(1)
406              Analyze the eigenvectors
407
408       gmx-covar(1)
409              Calculate and diagonalize the covariance matrix
410
411       gmx-make_edi(1)
412              Generate input files for essential dynamics sampling
413
414   Normal modes
415       gmx-anaeig(1)
416              Analyze the normal modes
417
418       gmx-nmeig(1)
419              Diagonalize the Hessian for normal mode analysis
420
421       gmx-nmtraj(1)
422              Generate a virtual oscillating trajectory from an eigenvector
423
424       gmx-nmens(1)
425              Generate an ensemble of structures from the normal modes
426
427       gmx-grompp(1)
428              Make a run input file
429
430       gmx-mdrun(1)
431              Find a potential energy minimum and calculate the Hessian
432
434       2019, GROMACS development team
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4392019.2                           Apr 16, 2019                           GMX(1)
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