3 <TITLE>GROMACS
4.5 Online Reference
</TITLE>
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12 <a href=
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23 Thu
26 Aug
2010</B></td>
29 <TABLE BORDER=
0 CELLSPACING=
0 CELLPADDING=
10>
31 <TD VALIGN=top
WIDTH=
"25%">
33 <A HREF=
"online/getting_started.html">Getting Started
</a>
35 <A HREF=
"online/flow.html">Flow Chart
</a>
37 <A HREF=
"online/files.html">File Formats
</a>
39 <A HREF=
"online/mdp_opt.html">mdp options
</a>
41 <A HREF=
"gmxfaq.html">FAQ
</a>
44 <TD VALIGN=top WIDTH=
75%
>
47 <A HREF=
"online/options.html">Options
</a>
49 <br><a href=online/demux.pl.html
>demux.pl
</a>
50 <br><a href=online/do_dssp.html
>do_dssp
</a>
51 <br><a href=online/editconf.html
>editconf
</a>
52 <br><a href=online/eneconv.html
>eneconv
</a>
53 <br><a href=online/g_anadock.html
>g_anadock
</a>
54 <br><a href=online/g_anaeig.html
>g_anaeig
</a>
55 <br><a href=online/g_analyze.html
>g_analyze
</a>
56 <br><a href=online/g_angle.html
>g_angle
</a>
57 <br><a href=online/g_bar.html
>g_bar
</a>
58 <br><a href=online/g_bond.html
>g_bond
</a>
59 <br><a href=online/g_bundle.html
>g_bundle
</a>
60 <br><a href=online/g_chi.html
>g_chi
</a>
61 <br><a href=online/g_cluster.html
>g_cluster
</a>
62 <br><a href=online/g_clustsize.html
>g_clustsize
</a>
63 <br><a href=online/g_confrms.html
>g_confrms
</a>
64 <br><a href=online/g_covar.html
>g_covar
</a>
65 <br><a href=online/g_current.html
>g_current
</a>
66 <br><a href=online/g_density.html
>g_density
</a>
67 <br><a href=online/g_densmap.html
>g_densmap
</a>
68 <br><a href=online/g_dielectric.html
>g_dielectric
</a>
69 <br><a href=online/g_dih.html
>g_dih
</a>
70 <br><a href=online/g_dipoles.html
>g_dipoles
</a>
71 <br><a href=online/g_disre.html
>g_disre
</a>
72 <br><a href=online/g_dist.html
>g_dist
</a>
73 <br><a href=online/g_dyndom.html
>g_dyndom
</a>
74 <br><a href=online/g_enemat.html
>g_enemat
</a>
75 <br><a href=online/g_energy.html
>g_energy
</a>
76 <br><a href=online/g_filter.html
>g_filter
</a>
77 <br><a href=online/g_gyrate.html
>g_gyrate
</a>
78 <br><a href=online/g_h2order.html
>g_h2order
</a>
79 <br><a href=online/g_hbond.html
>g_hbond
</a>
80 <br><a href=online/g_helix.html
>g_helix
</a>
81 <br><a href=online/g_helixorient.html
>g_helixorient
</a>
82 <br><a href=online/g_lie.html
>g_lie
</a>
83 <br><a href=online/g_luck.html
>g_luck
</a>
84 <br><a href=online/g_mdmat.html
>g_mdmat
</a>
85 <br><a href=online/g_membed.html
>g_membed
</a>
86 <br><a href=online/g_mindist.html
>g_mindist
</a>
87 <br><a href=online/g_morph.html
>g_morph
</a>
88 <br><a href=online/g_msd.html
>g_msd
</a>
89 <br><a href=online/g_nmeig.html
>g_nmeig
</a>
90 <br><a href=online/g_nmens.html
>g_nmens
</a>
91 <br><a href=online/g_nmtraj.html
>g_nmtraj
</a>
92 <br><a href=online/g_order.html
>g_order
</a>
93 <br><a href=online/g_polystat.html
>g_polystat
</a>
94 <br><a href=online/g_potential.html
>g_potential
</a>
95 <br><a href=online/g_principal.html
>g_principal
</a>
96 <br><a href=online/g_protonate.html
>g_protonate
</a>
97 <br><a href=online/g_rama.html
>g_rama
</a>
98 <br><a href=online/g_rdf.html
>g_rdf
</a>
99 <br><a href=online/g_rms.html
>g_rms
</a>
100 <br><a href=online/g_rmsdist.html
>g_rmsdist
</a>
101 <br><a href=online/g_rmsf.html
>g_rmsf
</a>
102 <br><a href=online/g_rotacf.html
>g_rotacf
</a>
103 <br><a href=online/g_rotmat.html
>g_rotmat
</a>
104 <br><a href=online/g_saltbr.html
>g_saltbr
</a>
105 <br><a href=online/g_sas.html
>g_sas
</a>
106 <br><a href=online/g_select.html
>g_select
</a>
107 <br><a href=online/g_sgangle.html
>g_sgangle
</a>
108 <br><a href=online/g_sham.html
>g_sham
</a>
109 <br><a href=online/g_sigeps.html
>g_sigeps
</a>
110 <br><a href=online/g_sorient.html
>g_sorient
</a>
111 <br><a href=online/g_spatial.html
>g_spatial
</a>
112 <br><a href=online/g_spol.html
>g_spol
</a>
113 <br><a href=online/g_tcaf.html
>g_tcaf
</a>
114 <br><a href=online/g_traj.html
>g_traj
</a>
115 <br><a href=online/g_tune_pme.html
>g_tune_pme
</a>
116 <br><a href=online/g_vanhove.html
>g_vanhove
</a>
117 <br><a href=online/g_velacc.html
>g_velacc
</a>
118 <br><a href=online/g_wham.html
>g_wham
</a>
119 <br><a href=online/g_wheel.html
>g_wheel
</a>
120 <br><a href=online/g_x2top.html
>g_x2top
</a>
121 <br><a href=online/g_xrama.html
>g_xrama
</a>
122 <br><a href=online/genbox.html
>genbox
</a>
123 <br><a href=online/genconf.html
>genconf
</a>
124 <br><a href=online/genion.html
>genion
</a>
125 <br><a href=online/genrestr.html
>genrestr
</a>
126 <br><a href=online/gmxcheck.html
>gmxcheck
</a>
127 <br><a href=online/gmxdump.html
>gmxdump
</a>
128 <br><a href=online/grompp.html
>grompp
</a>
129 <br><a href=online/make_edi.html
>make_edi
</a>
130 <br><a href=online/make_ndx.html
>make_ndx
</a>
131 <br><a href=online/mdrun.html
>mdrun
</a>
132 <br><a href=online/mk_angndx.html
>mk_angndx
</a>
133 <br><a href=online/ngmx.html
>ngmx
</a>
134 <br><a href=online/pdb2gmx.html
>pdb2gmx
</a>
135 <br><a href=online/tpbconv.html
>tpbconv
</a>
136 <br><a href=online/trjcat.html
>trjcat
</a>
137 <br><a href=online/trjconv.html
>trjconv
</a>
138 <br><a href=online/trjorder.html
>trjorder
</a>
139 <br><a href=online/xplor2gmx.pl.html
>xplor2gmx.pl
</a>
140 <br><a href=online/xpm2ps.html
>xpm2ps
</a>
146 <h3>Programs by Topic
</h3>
148 <A HREF=
"#HNR1">Generating topologies and coordinates
</A><br>
149 <A HREF=
"#HNR2">Running a simulation
</A><br>
150 <A HREF=
"#HNR3">Viewing trajectories
</A><br>
151 <A HREF=
"#HNR4">Processing energies
</A><br>
152 <A HREF=
"#HNR5">Converting files
</A><br>
153 <A HREF=
"#HNR6">Tools
</A><br>
154 <A HREF=
"#HNR7">Distances between structures
</A><br>
155 <A HREF=
"#HNR8">Distances in structures over time
</A><br>
156 <A HREF=
"#HNR9">Mass distribution properties over time
</A><br>
157 <A HREF=
"#HNR10">Analyzing bonded interactions
</A><br>
158 <A HREF=
"#HNR11">Structural properties
</A><br>
159 <A HREF=
"#HNR12">Kinetic properties
</A><br>
160 <A HREF=
"#HNR13">Electrostatic properties
</A><br>
161 <A HREF=
"#HNR14">Protein specific analysis
</A><br>
162 <A HREF=
"#HNR15">Interfaces
</A><br>
163 <A HREF=
"#HNR16">Covariance analysis
</A><br>
164 <A HREF=
"#HNR17">Normal modes
</A><br>
168 <TABLE CELLSPACING=
1>
169 <TR><TD>
170 <TR><TD COLSPAN=
2><b>Generating topologies and coordinates
</b>
171 <TR><TD><A HREF=
"online/pdb2gmx.html">pdb2gmx
</A></TD><TD>converts pdb files to topology and coordinate files
</TD>
172 <TR><TD><A HREF=
"online/g_x2top.html">g_x2top
</A></TD><TD>generates a primitive topology from coordinates
</TD>
173 <TR><TD><A HREF=
"online/editconf.html">editconf
</A></TD><TD>edits the box and writes subgroups
</TD>
174 <TR><TD><A HREF=
"online/genbox.html">genbox
</A></TD><TD>solvates a system
</TD>
175 <TR><TD><A HREF=
"online/genion.html">genion
</A></TD><TD>generates mono atomic ions on energetically favorable positions
</TD>
176 <TR><TD><A HREF=
"online/genconf.html">genconf
</A></TD><TD>multiplies a conformation in 'random' orientations
</TD>
177 <TR><TD><A HREF=
"online/genrestr.html">genrestr
</A></TD><TD>generates position restraints or distance restraints for index groups
</TD>
178 <TR><TD><A HREF=
"online/g_protonate.html">g_protonate
</A></TD><TD>protonates structures
</TD>
182 <TABLE CELLSPACING=
1>
183 <TR><TD>
184 <TR><TD COLSPAN=
2><b>Running a simulation
</b>
185 <TR><TD><A HREF=
"online/grompp.html">grompp
</A></TD><TD>makes a run input file
</TD>
186 <TR><TD><A HREF=
"online/tpbconv.html">tpbconv
</A></TD><TD>makes a run input file for restarting a crashed run
</TD>
187 <TR><TD><A HREF=
"online/mdrun.html">mdrun
</A></TD><TD>performs a simulation, do a normal mode analysis or an energy minimization
</TD>
191 <TABLE CELLSPACING=
1>
192 <TR><TD>
193 <TR><TD COLSPAN=
2><b>Viewing trajectories
</b>
194 <TR><TD><A HREF=
"online/ngmx.html">ngmx
</A></TD><TD>displays a trajectory
</TD>
195 <TR><TD><A HREF=
"online/g_highway.html">g_highway
</A></TD><TD>X Window System gadget for highway simulations
</TD>
196 <TR><TD><A HREF=
"online/g_nmtraj.html">g_nmtraj
</A></TD><TD>generate a virtual trajectory from an eigenvector
</TD>
200 <TABLE CELLSPACING=
1>
201 <TR><TD>
202 <TR><TD COLSPAN=
2><b>Processing energies
</b>
203 <TR><TD><A HREF=
"online/g_energy.html">g_energy
</A></TD><TD>writes energies to xvg files and displays averages
</TD>
204 <TR><TD><A HREF=
"online/g_enemat.html">g_enemat
</A></TD><TD>extracts an energy matrix from an energy file
</TD>
205 <TR><TD><A HREF=
"online/mdrun.html">mdrun
</A></TD><TD>with -rerun (re)calculates energies for trajectory frames
</TD>
209 <TABLE CELLSPACING=
1>
210 <TR><TD>
211 <TR><TD COLSPAN=
2><b>Converting files
</b>
212 <TR><TD><A HREF=
"online/editconf.html">editconf
</A></TD><TD>converts and manipulates structure files
</TD>
213 <TR><TD><A HREF=
"online/trjconv.html">trjconv
</A></TD><TD>converts and manipulates trajectory files
</TD>
214 <TR><TD><A HREF=
"online/trjcat.html">trjcat
</A></TD><TD>concatenates trajectory files
</TD>
215 <TR><TD><A HREF=
"online/eneconv.html">eneconv
</A></TD><TD>converts energy files
</TD>
216 <TR><TD><A HREF=
"online/xpm2ps.html">xpm2ps
</A></TD><TD>converts XPM matrices to encapsulated postscript (or XPM)
</TD>
217 <TR><TD><A HREF=
"online/g_sigeps.html">g_sigeps
</A></TD><TD>convert c6/
12 or c6/cn combinations to and from sigma/epsilon
</TD>
221 <TABLE CELLSPACING=
1>
222 <TR><TD>
223 <TR><TD COLSPAN=
2><b>Tools
</b>
224 <TR><TD><A HREF=
"online/make_ndx.html">make_ndx
</A></TD><TD>makes index files
</TD>
225 <TR><TD><A HREF=
"online/mk_angndx.html">mk_angndx
</A></TD><TD>generates index files for g_angle
</TD>
226 <TR><TD><A HREF=
"online/gmxcheck.html">gmxcheck
</A></TD><TD>checks and compares files
</TD>
227 <TR><TD><A HREF=
"online/gmxdump.html">gmxdump
</A></TD><TD>makes binary files human readable
</TD>
228 <TR><TD><A HREF=
"online/g_traj.html">g_traj
</A></TD><TD>plots x, v and f of selected atoms/groups (and more) from a trajectory
</TD>
229 <TR><TD><A HREF=
"online/g_analyze.html">g_analyze
</A></TD><TD>analyzes data sets
</TD>
230 <TR><TD><A HREF=
"online/trjorder.html">trjorder
</A></TD><TD>orders molecules according to their distance to a group
</TD>
231 <TR><TD><A HREF=
"online/g_filter.html">g_filter
</A></TD><TD>frequency filters trajectories, useful for making smooth movies
</TD>
232 <TR><TD><A HREF=
"online/g_lie.html">g_lie
</A></TD><TD>free energy estimate from linear combinations
</TD>
233 <TR><TD><A HREF=
"online/g_dyndom.html">g_dyndom
</A></TD><TD>interpolate and extrapolate structure rotations
</TD>
234 <TR><TD><A HREF=
"online/g_morph.html">g_morph
</A></TD><TD>linear interpolation of conformations
</TD>
235 <TR><TD><A HREF=
"online/g_wham.html">g_wham
</A></TD><TD>weighted histogram analysis after umbrella sampling
</TD>
236 <TR><TD><A HREF=
"online/xpm2ps.html">xpm2ps
</A></TD><TD>convert XPM (XPixelMap) file to postscript
</TD>
237 <TR><TD><A HREF=
"online/g_sham.html">g_sham
</A></TD><TD>read/write xmgr and xvgr data sets
</TD>
238 <TR><TD><A HREF=
"online/g_spatial.html">g_spatial
</A></TD><TD>calculates the spatial distribution function
</TD>
239 <TR><TD><A HREF=
"online/g_select.html">g_select
</A></TD><TD>selects groups of atoms based on flexible textual selections
</TD>
240 <TR><TD><A HREF=
"online/g_tune_pme.html">g_tune_pme
</A></TD><TD>time mdrun as a function of PME nodes to optimize settings
</TD>
244 <TABLE CELLSPACING=
1>
245 <TR><TD>
246 <TR><TD COLSPAN=
2><b>Distances between structures
</b>
247 <TR><TD><A HREF=
"online/g_rms.html">g_rms
</A></TD><TD>calculates rmsd's with a reference structure and rmsd matrices
</TD>
248 <TR><TD><A HREF=
"online/g_confrms.html">g_confrms
</A></TD><TD>fits two structures and calculates the rmsd
</TD>
249 <TR><TD><A HREF=
"online/g_cluster.html">g_cluster
</A></TD><TD>clusters structures
</TD>
250 <TR><TD><A HREF=
"online/g_rmsf.html">g_rmsf
</A></TD><TD>calculates atomic fluctuations
</TD>
254 <TABLE CELLSPACING=
1>
255 <TR><TD>
256 <TR><TD COLSPAN=
2><b>Distances in structures over time
</b>
257 <TR><TD><A HREF=
"online/g_mindist.html">g_mindist
</A></TD><TD>calculates the minimum distance between two groups
</TD>
258 <TR><TD><A HREF=
"online/g_dist.html">g_dist
</A></TD><TD>calculates the distances between the centers of mass of two groups
</TD>
259 <TR><TD><A HREF=
"online/g_bond.html">g_bond
</A></TD><TD>calculates distances between atoms
</TD>
260 <TR><TD><A HREF=
"online/g_mdmat.html">g_mdmat
</A></TD><TD>calculates residue contact maps
</TD>
261 <TR><TD><A HREF=
"online/g_polystat.html">g_polystat
</A></TD><TD>calculates static properties of polymers
</TD>
262 <TR><TD><A HREF=
"online/g_rmsdist.html">g_rmsdist
</A></TD><TD>calculates atom pair distances averaged with power -
2, -
3 or -
6</TD>
266 <TABLE CELLSPACING=
1>
267 <TR><TD>
268 <TR><TD COLSPAN=
2><b>Mass distribution properties over time
</b>
269 <TR><TD><A HREF=
"online/g_traj.html">g_traj
</A></TD><TD>plots x, v, f, box, temperature and rotational energy
</TD>
270 <TR><TD><A HREF=
"online/g_gyrate.html">g_gyrate
</A></TD><TD>calculates the radius of gyration
</TD>
271 <TR><TD><A HREF=
"online/g_msd.html">g_msd
</A></TD><TD>calculates mean square displacements
</TD>
272 <TR><TD><A HREF=
"online/g_polystat.html">g_polystat
</A></TD><TD>calculates static properties of polymers
</TD>
273 <TR><TD><A HREF=
"online/g_rotacf.html">g_rotacf
</A></TD><TD>calculates the rotational correlation function for molecules
</TD>
274 <TR><TD><A HREF=
"online/g_rdf.html">g_rdf
</A></TD><TD>calculates radial distribution functions
</TD>
275 <TR><TD><A HREF=
"online/g_rotmat.html">g_rotmat
</A></TD><TD>plots the rotation matrix for fitting to a reference structure
</TD>
276 <TR><TD><A HREF=
"online/g_vanhove.html">g_vanhove
</A></TD><TD>calculates Van Hove displacement functions
</TD>
280 <TABLE CELLSPACING=
1>
281 <TR><TD>
282 <TR><TD COLSPAN=
2><b>Analyzing bonded interactions
</b>
283 <TR><TD><A HREF=
"online/g_bond.html">g_bond
</A></TD><TD>calculates bond length distributions
</TD>
284 <TR><TD><A HREF=
"online/mk_angndx.html">mk_angndx
</A></TD><TD>generates index files for g_angle
</TD>
285 <TR><TD><A HREF=
"online/g_angle.html">g_angle
</A></TD><TD>calculates distributions and correlations for angles and dihedrals
</TD>
286 <TR><TD><A HREF=
"online/g_dih.html">g_dih
</A></TD><TD>analyzes dihedral transitions
</TD>
290 <TABLE CELLSPACING=
1>
291 <TR><TD>
292 <TR><TD COLSPAN=
2><b>Structural properties
</b>
293 <TR><TD><A HREF=
"online/g_hbond.html">g_hbond
</A></TD><TD>computes and analyzes hydrogen bonds
</TD>
294 <TR><TD><A HREF=
"online/g_saltbr.html">g_saltbr
</A></TD><TD>computes salt bridges
</TD>
295 <TR><TD><A HREF=
"online/g_sas.html">g_sas
</A></TD><TD>computes solvent accessible surface area
</TD>
296 <TR><TD><A HREF=
"online/g_order.html">g_order
</A></TD><TD>computes the order parameter per atom for carbon tails
</TD>
297 <TR><TD><A HREF=
"online/g_principal.html">g_principal
</A></TD><TD>calculates axes of inertia for a group of atoms
</TD>
298 <TR><TD><A HREF=
"online/g_rdf.html">g_rdf
</A></TD><TD>calculates radial distribution functions
</TD>
299 <TR><TD><A HREF=
"online/g_sgangle.html">g_sgangle
</A></TD><TD>computes the angle and distance between two groups
</TD>
300 <TR><TD><A HREF=
"online/g_sorient.html">g_sorient
</A></TD><TD>analyzes solvent orientation around solutes
</TD>
301 <TR><TD><A HREF=
"online/g_spol.html">g_spol
</A></TD><TD>analyzes solvent dipole orientation and polarization around solutes
</TD>
302 <TR><TD><A HREF=
"online/g_bundle.html">g_bundle
</A></TD><TD>analyzes bundles of axes, e.g. helices
</TD>
303 <TR><TD><A HREF=
"online/g_disre.html">g_disre
</A></TD><TD>analyzes distance restraints
</TD>
304 <TR><TD><A HREF=
"online/g_clustsize.html">g_clustsize
</A></TD><TD>calculate size distributions of atomic clusters
</TD>
305 <TR><TD><A HREF=
"online/g_anadock.html">g_anadock
</A></TD><TD>cluster structures from Autodock runs
</TD>
309 <TABLE CELLSPACING=
1>
310 <TR><TD>
311 <TR><TD COLSPAN=
2><b>Kinetic properties
</b>
312 <TR><TD><A HREF=
"online/g_traj.html">g_traj
</A></TD><TD>plots x, v, f, box, temperature and rotational energy
</TD>
313 <TR><TD><A HREF=
"online/g_velacc.html">g_velacc
</A></TD><TD>calculates velocity autocorrelation functions
</TD>
314 <TR><TD><A HREF=
"online/g_tcaf.html">g_tcaf
</A></TD><TD>calculates viscosities of liquids
</TD>
315 <TR><TD><A HREF=
"online/g_bar.html">g_bar
</A></TD><TD>calculates free energy difference estimates through Bennett's acceptance ratio
</TD>
316 <TR><TD><A HREF=
"online/g_current.html">g_current
</A></TD><TD>calculate current autocorrelation function of system
</TD>
317 <TR><TD><A HREF=
"online/g_vanhove.html">g_vanhove
</A></TD><TD>compute Van Hove correlation function
</TD>
318 <TR><TD><A HREF=
"online/g_principal.html">g_principal
</A></TD><TD>calculate principal axes of inertion for a group of atoms
</TD>
322 <TABLE CELLSPACING=
1>
323 <TR><TD>
324 <TR><TD COLSPAN=
2><b>Electrostatic properties
</b>
325 <TR><TD><A HREF=
"online/genion.html">genion
</A></TD><TD>generates mono atomic ions on energetically favorable positions
</TD>
326 <TR><TD><A HREF=
"online/g_potential.html">g_potential
</A></TD><TD>calculates the electrostatic potential across the box
</TD>
327 <TR><TD><A HREF=
"online/g_dipoles.html">g_dipoles
</A></TD><TD>computes the total dipole plus fluctuations
</TD>
328 <TR><TD><A HREF=
"online/g_dielectric.html">g_dielectric
</A></TD><TD>calculates frequency dependent dielectric constants
</TD>
329 <TR><TD><A HREF=
"online/g_current.html">g_current
</A></TD><TD>calculates dielectric constants for charged systems
</TD>
330 <TR><TD><A HREF=
"online/g_spol.html">g_spol
</A></TD><TD>analyze dipoles around a solute
</TD>
334 <TABLE CELLSPACING=
1>
335 <TR><TD>
336 <TR><TD COLSPAN=
2><b>Protein specific analysis
</b>
337 <TR><TD><A HREF=
"online/do_dssp.html">do_dssp
</A></TD><TD>assigns secondary structure and calculates solvent accessible surface area
</TD>
338 <TR><TD><A HREF=
"online/g_chi.html">g_chi
</A></TD><TD>calculates everything you want to know about chi and other dihedrals
</TD>
339 <TR><TD><A HREF=
"online/g_helix.html">g_helix
</A></TD><TD>calculates basic properties of alpha helices
</TD>
340 <TR><TD><A HREF=
"online/g_helixorient.html">g_helixorient
</A></TD><TD>calculates local pitch/bending/rotation/orientation inside helices
</TD>
341 <TR><TD><A HREF=
"online/g_rama.html">g_rama
</A></TD><TD>computes Ramachandran plots
</TD>
342 <TR><TD><A HREF=
"online/g_xrama.html">g_xrama
</A></TD><TD>shows animated Ramachandran plots
</TD>
343 <TR><TD><A HREF=
"online/g_wheel.html">g_wheel
</A></TD><TD>plots helical wheels
</TD>
347 <TABLE CELLSPACING=
1>
348 <TR><TD>
349 <TR><TD COLSPAN=
2><b>Interfaces
</b>
350 <TR><TD><A HREF=
"online/g_potential.html">g_potential
</A></TD><TD>calculates the electrostatic potential across the box
</TD>
351 <TR><TD><A HREF=
"online/g_density.html">g_density
</A></TD><TD>calculates the density of the system
</TD>
352 <TR><TD><A HREF=
"online/g_densmap.html">g_densmap
</A></TD><TD>calculates
2D planar or axial-radial density maps
</TD>
353 <TR><TD><A HREF=
"online/g_order.html">g_order
</A></TD><TD>computes the order parameter per atom for carbon tails
</TD>
354 <TR><TD><A HREF=
"online/g_h2order.html">g_h2order
</A></TD><TD>computes the orientation of water molecules
</TD>
355 <TR><TD><A HREF=
"online/g_bundle.html">g_bundle
</A></TD><TD>analyzes bundles of axes, e.g. transmembrane helices
</TD>
356 <TR><TD><A HREF=
"online/g_membed.html">g_membed
</A></TD><TD>embeds a protein into a lipid bilayer
</TD>
360 <TABLE CELLSPACING=
1>
361 <TR><TD>
362 <TR><TD COLSPAN=
2><b>Covariance analysis
</b>
363 <TR><TD><A HREF=
"online/g_covar.html">g_covar
</A></TD><TD>calculates and diagonalizes the covariance matrix
</TD>
364 <TR><TD><A HREF=
"online/g_anaeig.html">g_anaeig
</A></TD><TD>analyzes the eigenvectors
</TD>
365 <TR><TD><A HREF=
"online/make_edi.html">make_edi
</A></TD><TD>generate input files for essential dynamics sampling
</TD>
369 <TABLE CELLSPACING=
1>
370 <TR><TD>
371 <TR><TD COLSPAN=
2><b>Normal modes
</b>
372 <TR><TD><A HREF=
"online/grompp.html">grompp
</A></TD><TD>makes a run input file
</TD>
373 <TR><TD><A HREF=
"online/mdrun.html">mdrun
</A></TD><TD>finds a potential energy minimum
</TD>
374 <TR><TD><A HREF=
"online/mdrun.html">mdrun
</A></TD><TD>calculates the Hessian
</TD>
375 <TR><TD><A HREF=
"online/g_nmeig.html">g_nmeig
</A></TD><TD>diagonalizes the Hessian
</TD>
376 <TR><TD><A HREF=
"online/g_nmtraj.html">g_nmtraj
</A></TD><TD>generate oscillating trajectory of an eigenmode
</TD>
377 <TR><TD><A HREF=
"online/g_anaeig.html">g_anaeig
</A></TD><TD>analyzes the normal modes
</TD>
378 <TR><TD><A HREF=
"online/g_nmens.html">g_nmens
</A></TD><TD>generates an ensemble of structures from the normal modes
</TD>
383 <font size=
"-1"><a href=
"http://www.gromacs.org">http://www.gromacs.org
</a></font><br>