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  12 <a href="http://www.gromacs.org/">
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  15 <br><br>
  16 <h2>
  17 GROMACS 3.3<br>
  18 Online Reference</h2>
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  21 <td ALIGN=RIGHT VALIGN=BOTTOM WIDTH="*" NOSAVE>
  22 <B>VERSION 4.0<br>
  23 Sun 18 Jan 2009</B></td>
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  25 </table>
  26
  27 <hr>
  28
  29 <TABLE BORDER=0 CELLSPACING=0 CELLPADDING=10>
  30 <TR>
  31 <TD VALIGN=top WIDTH="25%">
  32 <h3>General</h3>
  33 <A HREF="online/getting_started.html">Getting Started</a>
  34 <br><br>
  35 <A HREF="online/flow.html">Flow Chart</a>
  36 <br><br>
  37 <A HREF="online/files.html">File Formats</a>
  38 <br><br>
  39 <A HREF="online/mdp_opt.html">mdp options</a>
  40 <br><br>
  41 <A HREF="gmxfaq.html">FAQ</a>
  42 <br>
  43 </TD>
  44 <TD VALIGN=top WIDTH=75%>
  45 <h3>Programs</h3>
  46 <multicol cols=5>
  47 <A HREF="online/options.html">Options</a>
  48 <br>
  49 <br><a href=online/anadock.html>anadock</a>
  50 <br><a href=online/demux.pl.html>demux.pl</a>
  51 <br><a href=online/do_dssp.html>do_dssp</a>
  52 <br><a href=online/editconf.html>editconf</a>
  53 <br><a href=online/eneconv.html>eneconv</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_bond.html>g_bond</a>
  58 <br><a href=online/g_bundle.html>g_bundle</a>
  59 <br><a href=online/g_chi.html>g_chi</a>
  60 <br><a href=online/g_cluster.html>g_cluster</a>
  61 <br><a href=online/g_clustsize.html>g_clustsize</a>
  62 <br><a href=online/g_confrms.html>g_confrms</a>
  63 <br><a href=online/g_covar.html>g_covar</a>
  64 <br><a href=online/g_current.html>g_current</a>
  65 <br><a href=online/g_density.html>g_density</a>
  66 <br><a href=online/g_densmap.html>g_densmap</a>
  67 <br><a href=online/g_dielectric.html>g_dielectric</a>
  68 <br><a href=online/g_dih.html>g_dih</a>
  69 <br><a href=online/g_dipoles.html>g_dipoles</a>
  70 <br><a href=online/g_disre.html>g_disre</a>
  71 <br><a href=online/g_dist.html>g_dist</a>
  72 <br><a href=online/g_dyndom.html>g_dyndom</a>
  73 <br><a href=online/g_enemat.html>g_enemat</a>
  74 <br><a href=online/g_energy.html>g_energy</a>
  75 <br><a href=online/g_filter.html>g_filter</a>
  76 <br><a href=online/g_gyrate.html>g_gyrate</a>
  77 <br><a href=online/g_h2order.html>g_h2order</a>
  78 <br><a href=online/g_hbond.html>g_hbond</a>
  79 <br><a href=online/g_helix.html>g_helix</a>
  80 <br><a href=online/g_helixorient.html>g_helixorient</a>
  81 <br><a href=online/g_kinetics.html>g_kinetics</a>
  82 <br><a href=online/g_lie.html>g_lie</a>
  83 <br><a href=online/g_mdmat.html>g_mdmat</a>
  84 <br><a href=online/g_mindist.html>g_mindist</a>
  85 <br><a href=online/g_morph.html>g_morph</a>
  86 <br><a href=online/g_msd.html>g_msd</a>
  87 <br><a href=online/g_nmeig.html>g_nmeig</a>
  88 <br><a href=online/g_nmens.html>g_nmens</a>
  89 <br><a href=online/g_nmtraj.html>g_nmtraj</a>
  90 <br><a href=online/g_order.html>g_order</a>
  91 <br><a href=online/g_polystat.html>g_polystat</a>
  92 <br><a href=online/g_potential.html>g_potential</a>
  93 <br><a href=online/g_principal.html>g_principal</a>
  94 <br><a href=online/g_rama.html>g_rama</a>
  95 <br><a href=online/g_rdf.html>g_rdf</a>
  96 <br><a href=online/g_rms.html>g_rms</a>
  97 <br><a href=online/g_rmsdist.html>g_rmsdist</a>
  98 <br><a href=online/g_rmsf.html>g_rmsf</a>
  99 <br><a href=online/g_rotacf.html>g_rotacf</a>
 100 <br><a href=online/g_saltbr.html>g_saltbr</a>
 101 <br><a href=online/g_sas.html>g_sas</a>
 102 <br><a href=online/g_sdf.html>g_sdf</a>
 103 <br><a href=online/g_sgangle.html>g_sgangle</a>
 104 <br><a href=online/g_sham.html>g_sham</a>
 105 <br><a href=online/g_sorient.html>g_sorient</a>
 106 <br><a href=online/g_spatial.html>g_spatial</a>
 107 <br><a href=online/g_spol.html>g_spol</a>
 108 <br><a href=online/g_tcaf.html>g_tcaf</a>
 109 <br><a href=online/g_traj.html>g_traj</a>
 110 <br><a href=online/g_vanhove.html>g_vanhove</a>
 111 <br><a href=online/g_velacc.html>g_velacc</a>
 112 <br><a href=online/g_wham.html>g_wham</a>
 113 <br><a href=online/genbox.html>genbox</a>
 114 <br><a href=online/genconf.html>genconf</a>
 115 <br><a href=online/genion.html>genion</a>
 116 <br><a href=online/genrestr.html>genrestr</a>
 117 <br><a href=online/gmxcheck.html>gmxcheck</a>
 118 <br><a href=online/gmxdump.html>gmxdump</a>
 119 <br><a href=online/grompp.html>grompp</a>
 120 <br><a href=online/highway.html>highway</a>
 121 <br><a href=online/make_edi.html>make_edi</a>
 122 <br><a href=online/make_ndx.html>make_ndx</a>
 123 <br><a href=online/mdrun.html>mdrun</a>
 124 <br><a href=online/mk_angndx.html>mk_angndx</a>
 125 <br><a href=online/ngmx.html>ngmx</a>
 126 <br><a href=online/pdb2gmx.html>pdb2gmx</a>
 127 <br><a href=online/protonate.html>protonate</a>
 128 <br><a href=online/sigeps.html>sigeps</a>
 129 <br><a href=online/tpbconv.html>tpbconv</a>
 130 <br><a href=online/trjcat.html>trjcat</a>
 131 <br><a href=online/trjconv.html>trjconv</a>
 132 <br><a href=online/trjorder.html>trjorder</a>
 133 <br><a href=online/wheel.html>wheel</a>
 134 <br><a href=online/x2top.html>x2top</a>
 135 <br><a href=online/xplor2gmx.pl.html>xplor2gmx.pl</a>
 136 <br><a href=online/xpm2ps.html>xpm2ps</a>
 137 <br><a href=online/xrama.html>xrama</a>
 138 </multicol>
 139 </TD>
 140 </TR>
 141 </TABLE>
 142 <HR>
 143 <h3>Programs by Topic</h3>
 144 <multicol cols=3>
 145 <A HREF="#HNR1">Generating topologies and coordinates</A><br>
 146 <A HREF="#HNR2">Running a simulation</A><br>
 147 <A HREF="#HNR3">Viewing trajectories</A><br>
 148 <A HREF="#HNR4">Processing energies</A><br>
 149 <A HREF="#HNR5">Converting files</A><br>
 150 <A HREF="#HNR6">Tools</A><br>
 151 <A HREF="#HNR7">Distances between structures</A><br>
 152 <A HREF="#HNR8">Distances in structures over time</A><br>
 153 <A HREF="#HNR9">Mass distribution properties over time</A><br>
 154 <A HREF="#HNR10">Analyzing bonded interactions</A><br>
 155 <A HREF="#HNR11">Structural properties</A><br>
 156 <A HREF="#HNR12">Kinetic properties</A><br>
 157 <A HREF="#HNR13">Electrostatic properties</A><br>
 158 <A HREF="#HNR14">Protein specific analysis</A><br>
 159 <A HREF="#HNR15">Interfaces</A><br>
 160 <A HREF="#HNR16">Covariance analysis</A><br>
 161 <A HREF="#HNR17">Normal modes</A><br>
 162 </multicol>
 163
 164 <A NAME="HNR1">
 165 <TABLE CELLSPACING=1>
 166 <TR><TD>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 167 <TR><TD COLSPAN=2><b>Generating topologies and coordinates</b>
 168 <TR><TD><A HREF="online/pdb2gmx.html">pdb2gmx</A></TD><TD>converts pdb files to topology and coordinate files</TD>
 169 <TR><TD><A HREF="online/x2top.html">x2top</A></TD><TD>generates a primitive topology from coordinates </TD>
 170 <TR><TD><A HREF="online/editconf.html">editconf</A></TD><TD>edits the box and writes subgroups </TD>
 171 <TR><TD><A HREF="online/genbox.html">genbox</A></TD><TD>solvates a system</TD>
 172 <TR><TD><A HREF="online/genion.html">genion</A></TD><TD>generates mono atomic ions on energetically favorable positions</TD>
 173 <TR><TD><A HREF="online/genconf.html">genconf</A></TD><TD>multiplies a conformation in 'random' orientations</TD>
 174 <TR><TD><A HREF="online/genrestr.html">genrestr</A></TD><TD>generates position restraints or distance restraints for index groups</TD>
 175 <TR><TD><A HREF="online/protonate.html">protonate</A></TD><TD>protonates structures</TD>
 176 </TABLE>
 177
 178 <A NAME="HNR2">
 179 <TABLE CELLSPACING=1>
 180 <TR><TD>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 181 <TR><TD COLSPAN=2><b>Running a simulation</b>
 182 <TR><TD><A HREF="online/grompp.html">grompp</A></TD><TD>makes a run input file</TD>
 183 <TR><TD><A HREF="online/tpbconv.html">tpbconv</A></TD><TD>makes a run input file for restarting a crashed run</TD>
 184 <TR><TD><A HREF="online/mdrun.html">mdrun</A></TD><TD>performs a simulation</TD>
 185 </TABLE>
 186
 187 <A NAME="HNR3">
 188 <TABLE CELLSPACING=1>
 189 <TR><TD>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 190 <TR><TD COLSPAN=2><b>Viewing trajectories</b>
 191 <TR><TD><A HREF="online/ngmx.html">ngmx</A></TD><TD>displays a trajectory</TD>
 192 <TR><TD><A HREF="online/trjconv.html">trjconv</A></TD><TD>converts trajectories to e.g. pdb which can be viewed with e.g. rasmol</TD>
 193 </TABLE>
 194
 195 <A NAME="HNR4">
 196 <TABLE CELLSPACING=1>
 197 <TR><TD>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 198 <TR><TD COLSPAN=2><b>Processing energies</b>
 199 <TR><TD><A HREF="online/g_energy.html">g_energy</A></TD><TD>writes energies to xvg files and displays averages</TD>
 200 <TR><TD><A HREF="online/g_enemat.html">g_enemat</A></TD><TD>extracts an energy matrix from an energy file</TD>
 201 <TR><TD><A HREF="online/mdrun.html">mdrun</A></TD><TD>with -rerun (re)calculates energies for trajectory frames</TD>
 202 </TABLE>
 203
 204 <A NAME="HNR5">
 205 <TABLE CELLSPACING=1>
 206 <TR><TD>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 207 <TR><TD COLSPAN=2><b>Converting files</b>
 208 <TR><TD><A HREF="online/editconf.html">editconf</A></TD><TD>converts and manipulates structure files</TD>
 209 <TR><TD><A HREF="online/trjconv.html">trjconv</A></TD><TD>converts and manipulates trajectory files</TD>
 210 <TR><TD><A HREF="online/trjcat.html">trjcat</A></TD><TD>concatenates trajectory files</TD>
 211 <TR><TD><A HREF="online/eneconv.html">eneconv</A></TD><TD>converts energy files</TD>
 212 <TR><TD><A HREF="online/xmp2ps.html">xmp2ps</A></TD><TD>converts XPM matrices to encapsulated postscript (or XPM)</TD>
 213 </TABLE>
 214
 215 <A NAME="HNR6">
 216 <TABLE CELLSPACING=1>
 217 <TR><TD>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 218 <TR><TD COLSPAN=2><b>Tools</b>
 219 <TR><TD><A HREF="online/make_ndx.html">make_ndx</A></TD><TD>makes index files</TD>
 220 <TR><TD><A HREF="online/mk_angndx.html">mk_angndx</A></TD><TD>generates index files for g_angle</TD>
 221 <TR><TD><A HREF="online/gmxcheck.html">gmxcheck</A></TD><TD>checks and compares files</TD>
 222 <TR><TD><A HREF="online/gmxdump.html">gmxdump</A></TD><TD>makes binary files human readable</TD>
 223 <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>
 224 <TR><TD><A HREF="online/g_analyze.html">g_analyze</A></TD><TD>analyzes data sets</TD>
 225 <TR><TD><A HREF="online/trjorder.html">trjorder</A></TD><TD>orders molecules according to their distance to a group</TD>
 226 <TR><TD><A HREF="online/g_filter.html">g_filter</A></TD><TD>frequency filters trajectories, useful for making smooth movies</TD>
 227 <TR><TD><A HREF="online/g_lie.html">g_lie</A></TD><TD>free energy estimate from linear combinations</TD>
 228 <TR><TD><A HREF="online/g_dyndom.html">g_dyndom</A></TD><TD>interpolate and extrapolate structure rotations</TD>
 229 <TR><TD><A HREF="online/g_morph.html">g_morph</A></TD><TD>linear interpolation of conformations </TD>
 230 <TR><TD><A HREF="online/g_wham.html">g_wham</A></TD><TD>weighted histogram analysis after umbrella sampling</TD>
 231 <TR><TD><A HREF="online/ffscan.html">ffscan</A></TD><TD>scan and modify force field data for a single point energy calculation</TD>
 232 <TR><TD><A HREF="online/xpm2ps.html">xpm2ps</A></TD><TD>convert XPM (XPixelMap) file to postscript</TD>
 233 </TABLE>
 234
 235 <A NAME="HNR7">
 236 <TABLE CELLSPACING=1>
 237 <TR><TD>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 238 <TR><TD COLSPAN=2><b>Distances between structures</b>
 239 <TR><TD><A HREF="online/g_rms.html">g_rms</A></TD><TD>calculates rmsd's with a reference structure and rmsd matrices</TD>
 240 <TR><TD><A HREF="online/g_confrms.html">g_confrms</A></TD><TD>fits two structures and calculates the rmsd </TD>
 241 <TR><TD><A HREF="online/g_cluster.html">g_cluster</A></TD><TD>clusters structures</TD>
 242 <TR><TD><A HREF="online/g_rmsf.html">g_rmsf</A></TD><TD>calculates atomic fluctuations</TD>
 243 <TR><TD><A HREF="online/disco.html">disco</A></TD><TD>distance geometry calculation with the CONCOORD algorithm</TD>
 244 <TR><TD><A HREF="online/cdist.html">cdist</A></TD><TD>create input for disco</TD>
 245 </TABLE>
 246
 247 <A NAME="HNR8">
 248 <TABLE CELLSPACING=1>
 249 <TR><TD>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 250 <TR><TD COLSPAN=2><b>Distances in structures over time</b>
 251 <TR><TD><A HREF="online/g_mindist.html">g_mindist</A></TD><TD>calculates the minimum distance between two groups</TD>
 252 <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>
 253 <TR><TD><A HREF="online/g_bond.html">g_bond</A></TD><TD>calculates distances between atoms</TD>
 254 <TR><TD><A HREF="online/g_mdmat.html">g_mdmat</A></TD><TD>calculates residue contact maps</TD>
 255 <TR><TD><A HREF="online/g_polystat.html">g_polystat</A></TD><TD>calculates static properties of polymers</TD>
 256 <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>
 257 </TABLE>
 258
 259 <A NAME="HNR9">
 260 <TABLE CELLSPACING=1>
 261 <TR><TD>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 262 <TR><TD COLSPAN=2><b>Mass distribution properties over time</b>
 263 <TR><TD><A HREF="online/g_traj.html">g_traj</A></TD><TD>plots x, v, f, box, temperature and rotational energy</TD>
 264 <TR><TD><A HREF="online/g_gyrate.html">g_gyrate</A></TD><TD>calculates the radius of gyration</TD>
 265 <TR><TD><A HREF="online/g_msd.html">g_msd</A></TD><TD>calculates mean square displacements</TD>
 266 <TR><TD><A HREF="online/g_polystat.html">g_polystat</A></TD><TD>calculates static properties of polymers</TD>
 267 <TR><TD><A HREF="online/g_rotacf.html">g_rotacf</A></TD><TD>calculates the rotational correlation function for molecules</TD>
 268 <TR><TD><A HREF="online/g_vanhove.html">g_vanhove</A></TD><TD>calculates Van Hove displacement functions</TD>
 269 </TABLE>
 270
 271 <A NAME="HNR10">
 272 <TABLE CELLSPACING=1>
 273 <TR><TD>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 274 <TR><TD COLSPAN=2><b>Analyzing bonded interactions</b>
 275 <TR><TD><A HREF="online/g_bond.html">g_bond</A></TD><TD>calculates bond length distributions</TD>
 276 <TR><TD><A HREF="online/mk_angndx.html">mk_angndx</A></TD><TD>generates index files for g_angle</TD>
 277 <TR><TD><A HREF="online/g_angle.html">g_angle</A></TD><TD>calculates distributions and correlations for angles and dihedrals</TD>
 278 <TR><TD><A HREF="online/g_dih.html">g_dih</A></TD><TD>analyzes dihedral transitions</TD>
 279 </TABLE>
 280
 281 <A NAME="HNR11">
 282 <TABLE CELLSPACING=1>
 283 <TR><TD>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 284 <TR><TD COLSPAN=2><b>Structural properties</b>
 285 <TR><TD><A HREF="online/g_hbond.html">g_hbond</A></TD><TD>computes and analyzes hydrogen bonds</TD>
 286 <TR><TD><A HREF="online/g_saltbr.html">g_saltbr</A></TD><TD>computes salt bridges</TD>
 287 <TR><TD><A HREF="online/g_sas.html">g_sas</A></TD><TD>computes solvent accessible surface area</TD>
 288 <TR><TD><A HREF="online/g_order.html">g_order</A></TD><TD>computes the order parameter per atom for carbon tails</TD>
 289 <TR><TD><A HREF="online/g_principal.html">g_principal</A></TD><TD>calculates axes of inertia for a group of atoms</TD>
 290 <TR><TD><A HREF="online/g_rdf.html">g_rdf</A></TD><TD>calculates radial distribution functions</TD>
 291 <TR><TD><A HREF="online/g_sdf.html">g_sdf</A></TD><TD>calculates solvent distribution functions</TD>
 292 <TR><TD><A HREF="online/g_sgangle.html">g_sgangle</A></TD><TD>computes the angle and distance between two groups</TD>
 293 <TR><TD><A HREF="online/g_sorient.html">g_sorient</A></TD><TD>analyzes solvent orientation around solutes</TD>
 294 <TR><TD><A HREF="online/g_spol.html">g_spol</A></TD><TD>analyzes solvent dipole orientation and polarization around solutes</TD>
 295 <TR><TD><A HREF="online/g_bundle.html">g_bundle</A></TD><TD>analyzes bundles of axes, e.g. helices</TD>
 296 <TR><TD><A HREF="online/g_disre.html">g_disre</A></TD><TD>analyzes distance restraints</TD>
 297 <TR><TD><A HREF="online/g_clustsize.html">g_clustsize</A></TD><TD>calculate size distributions of atomic clusters</TD>
 298 <TR><TD><A HREF="online/disco.html">disco</A></TD><TD>distance geometry calculation with the CONCOORD algorithm</TD>
 299 <TR><TD><A HREF="online/cdist.html">cdist</A></TD><TD>create input for disco</TD>
 300 <TR><TD><A HREF="online/anadock.html">anadock</A></TD><TD>cluster structures from Autodock runs</TD>
 301 </TABLE>
 302
 303 <A NAME="HNR12">
 304 <TABLE CELLSPACING=1>
 305 <TR><TD>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 306 <TR><TD COLSPAN=2><b>Kinetic properties</b>
 307 <TR><TD><A HREF="online/g_traj.html">g_traj</A></TD><TD>plots x, v, f, box, temperature and rotational energy</TD>
 308 <TR><TD><A HREF="online/g_velacc.html">g_velacc</A></TD><TD>calculates velocity autocorrelation functions</TD>
 309 <TR><TD><A HREF="online/g_tcaf.html">g_tcaf</A></TD><TD>calculates viscosities of liquids</TD>
 310 <TR><TD><A HREF="online/g_kinetics.html">g_kinetics</A></TD><TD>derives information about kinetic processes from you trajectories</TD>
 311 </TABLE>
 312
 313 <A NAME="HNR13">
 314 <TABLE CELLSPACING=1>
 315 <TR><TD>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 316 <TR><TD COLSPAN=2><b>Electrostatic properties</b>
 317 <TR><TD><A HREF="online/genion.html">genion</A></TD><TD>generates mono atomic ions on energetically favorable positions</TD>
 318 <TR><TD><A HREF="online/g_potential.html">g_potential</A></TD><TD>calculates the electrostatic potential across the box</TD>
 319 <TR><TD><A HREF="online/g_dipoles.html">g_dipoles</A></TD><TD>computes the total dipole plus fluctuations</TD>
 320 <TR><TD><A HREF="online/g_dielectric.html">g_dielectric</A></TD><TD>calculates frequency dependent dielectric constants</TD>
 321 <TR><TD><A HREF="online/g_current.html">g_current</A></TD><TD>calculates dielectric constants for charged systems</TD>
 322 </TABLE>
 323
 324 <A NAME="HNR14">
 325 <TABLE CELLSPACING=1>
 326 <TR><TD>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 327 <TR><TD COLSPAN=2><b>Protein specific analysis</b>
 328 <TR><TD><A HREF="online/do_dssp.html">do_dssp</A></TD><TD>assigns secondary structure and calculates solvent accessible surface area</TD>
 329 <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>
 330 <TR><TD><A HREF="online/g_helix.html">g_helix</A></TD><TD>calculates basic properties of alpha helices</TD>
 331 <TR><TD><A HREF="online/g_helixorient.html">g_helixorient</A></TD><TD>calculates local pitch/bending/rotation/orientation inside helices</TD>
 332 <TR><TD><A HREF="online/g_rama.html">g_rama</A></TD><TD>computes Ramachandran plots</TD>
 333 <TR><TD><A HREF="online/xrama.html">xrama</A></TD><TD>shows animated Ramachandran plots</TD>
 334 <TR><TD><A HREF="online/wheel.html">wheel</A></TD><TD>plots helical wheels</TD>
 335 </TABLE>
 336
 337 <A NAME="HNR15">
 338 <TABLE CELLSPACING=1>
 339 <TR><TD>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 340 <TR><TD COLSPAN=2><b>Interfaces</b>
 341 <TR><TD><A HREF="online/g_potential.html">g_potential</A></TD><TD>calculates the electrostatic potential across the box</TD>
 342 <TR><TD><A HREF="online/g_density.html">g_density</A></TD><TD>calculates the density of the system</TD>
 343 <TR><TD><A HREF="online/g_densmap.html">g_densmap</A></TD><TD>calculates 2D planar or axial-radial density maps</TD>
 344 <TR><TD><A HREF="online/g_order.html">g_order</A></TD><TD>computes the order parameter per atom for carbon tails</TD>
 345 <TR><TD><A HREF="online/g_h2order.html">g_h2order</A></TD><TD>computes the orientation of water molecules</TD>
 346 <TR><TD><A HREF="online/g_bundle.html">g_bundle</A></TD><TD>analyzes bundles of axes, e.g. transmembrane helices</TD>
 347 </TABLE>
 348
 349 <A NAME="HNR16">
 350 <TABLE CELLSPACING=1>
 351 <TR><TD>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 352 <TR><TD COLSPAN=2><b>Covariance analysis</b>
 353 <TR><TD><A HREF="online/g_covar.html">g_covar</A></TD><TD>calculates and diagonalizes the covariance matrix</TD>
 354 <TR><TD><A HREF="online/g_anaeig.html">g_anaeig</A></TD><TD>analyzes the eigenvectors</TD>
 355 <TR><TD><A HREF="online/make_edi.html">make_edi</A></TD><TD>generate input files for essential dynamics sampling</TD>
 356 </TABLE>
 357
 358 <A NAME="HNR17">
 359 <TABLE CELLSPACING=1>
 360 <TR><TD>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 361 <TR><TD COLSPAN=2><b>Normal modes</b>
 362 <TR><TD><A HREF="online/grompp.html">grompp</A></TD><TD>makes a run input file</TD>
 363 <TR><TD><A HREF="online/mdrun.html">mdrun</A></TD><TD>finds a potential energy minimum</TD>
 364 <TR><TD><A HREF="online/mdrun.html">mdrun</A></TD><TD>calculates the Hessian</TD>
 365 <TR><TD><A HREF="online/g_nmeig.html">g_nmeig</A></TD><TD>diagonalizes the Hessian </TD>
 366 <TR><TD><A HREF="online/g_nmtraj.html">g_nmtraj</A></TD><TD>generate oscillating trajectory of an eigenmode</TD>
 367 <TR><TD><A HREF="online/g_anaeig.html">g_anaeig</A></TD><TD>analyzes the normal modes</TD>
 368 <TR><TD><A HREF="online/g_nmens.html">g_nmens</A></TD><TD>generates an ensemble of structures from the normal modes</TD>
 369 </TABLE>
 370 <p>
 371 <hr>
 372 <div ALIGN=RIGHT>
 373 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
 374 </body>
 375 </html>