2 <TITLE>GROMACS
2.0 Manual
</TITLE>
4 <H1>GROMACS
2.0 manual
</H1>
5 <IMG SRC=
"gif/rainbow.gif" WIDTH=
100% HEIGHT=
7>
7 <TABLE BORDER=
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9 <TD VALIGN=top WIDTH=
25%
>
11 <A HREF=
"online/getting_started.html">Getting Started
</a>
13 <A HREF=
"online/flow.html">Flow Chart
</a>
15 <A HREF=
"online/files.html">File Formats
</a>
17 <A HREF=
"online/mdp_opt.html">mdp options
</a>
19 <A HREF=
"gmxfaq.html">FAQ
</a>
21 <TD VALIGN=top WIDTH=
75%
>
24 <A HREF=
"online/options.html">Options
</a>
26 <br><a href=
"online/do_dssp.html">do_dssp
</a>
27 <br><a href=
"online/editconf.html">editconf
</a>
28 <br><a href=
"online/eneconv.html">eneconv
</a>
29 <br><a href=
"online/g_anaeig.html">g_anaeig
</a>
30 <br><a href=
"online/g_analyze.html">g_analyze
</a>
31 <br><a href=
"online/g_angle.html">g_angle
</a>
32 <br><a href=
"online/g_bond.html">g_bond
</a>
33 <br><a href=
"online/g_chi.html">g_chi
</a>
34 <br><a href=
"online/g_cluster.html">g_cluster
</a>
35 <br><a href=
"online/g_com.html">g_com
</a>
36 <br><a href=
"online/g_confrms.html">g_confrms
</a>
37 <br><a href=
"online/g_covar.html">g_covar
</a>
38 <br><a href=
"online/g_density.html">g_density
</a>
39 <br><a href=
"online/g_dielectric.html">g_dielectric
</a>
40 <br><a href=
"online/g_dih.html">g_dih
</a>
41 <br><a href=
"online/g_dipoles.html">g_dipoles
</a>
42 <br><a href=
"online/g_disre.html">g_disre
</a>
43 <br><a href=
"online/g_dist.html">g_dist
</a>
44 <br><a href=
"online/g_enemat.html">g_enemat
</a>
45 <br><a href=
"online/g_energy.html">g_energy
</a>
46 <br><a href=
"online/g_gyrate.html">g_gyrate
</a>
47 <br><a href=
"online/g_h2order.html">g_h2order
</a>
48 <br><a href=
"online/g_hbond.html">g_hbond
</a>
49 <br><a href=
"online/g_helix.html">g_helix
</a>
50 <br><a href=
"online/g_mdmat.html">g_mdmat
</a>
51 <br><a href=
"online/g_mindist.html">g_mindist
</a>
52 <br><a href=
"online/g_msd.html">g_msd
</a>
53 <br><a href=
"online/g_nmeig.html">g_nmeig
</a>
54 <br><a href=
"online/g_nmens.html">g_nmens
</a>
55 <br><a href=
"online/g_order.html">g_order
</a>
56 <br><a href=
"online/g_potential.html">g_potential
</a>
57 <br><a href=
"online/g_rama.html">g_rama
</a>
58 <br><a href=
"online/g_rdens.html">g_rdens
</a>
59 <br><a href=
"online/g_rdf.html">g_rdf
</a>
60 <br><a href=
"online/g_rms.html">g_rms
</a>
61 <br><a href=
"online/g_rmsdist.html">g_rmsdist
</a>
62 <br><a href=
"online/g_rmsf.html">g_rmsf
</a>
63 <br><a href=
"online/g_rotacf.html">g_rotacf
</a>
64 <br><a href=
"online/g_saltbr.html">g_saltbr
</a>
65 <br><a href=
"online/g_sas.html">g_sas
</a>
66 <br><a href=
"online/g_sgangle.html">g_sgangle
</a>
67 <br><a href=
"online/g_velacc.html">g_velacc
</a>
68 <br><a href=
"online/genbox.html">genbox
</a>
69 <br><a href=
"online/genconf.html">genconf
</a>
70 <br><a href=
"online/gendr.html">gendr
</a>
71 <br><a href=
"online/genion.html">genion
</a>
72 <br><a href=
"online/genpr.html">genpr
</a>
73 <br><a href=
"online/gmxcheck.html">gmxcheck
</a>
74 <br><a href=
"online/gmxdump.html">gmxdump
</a>
75 <br><a href=
"online/grompp.html">grompp
</a>
76 <br><a href=
"online/highway.html">highway
</a>
77 <br><a href=
"online/make_ndx.html">make_ndx
</a>
78 <br><a href=
"online/mdrun.html">mdrun
</a>
79 <br><a href=
"online/mk_angndx.html">mk_angndx
</a>
80 <br><a href=
"online/ngmx.html">ngmx
</a>
81 <br><a href=
"online/nmrun.html">nmrun
</a>
82 <br><a href=
"online/pdb2gmx.html">pdb2gmx
</a>
83 <br><a href=
"online/protonate.html">protonate
</a>
84 <br><a href=
"online/tpbconv.html">tpbconv
</a>
85 <br><a href=
"online/trjcat.html">trjcat
</a>
86 <br><a href=
"online/trjconv.html">trjconv
</a>
87 <br><a href=
"online/wheel.html">wheel
</a>
88 <br><a href=
"online/xpm2ps.html">xpm2ps
</a>
89 <br><a href=
"online/xrama.html">xrama
</a>
94 <IMG SRC=
"gif/rainbow.gif" WIDTH=
100% HEIGHT=
7>
95 <h3>Programs by Topic
</h3>
97 <A HREF=
"#HNR1">Generating topologies and coordinates
</A><br>
98 <A HREF=
"#HNR2">Running a simulation
</A><br>
99 <A HREF=
"#HNR3">Viewing trajectories
</A><br>
100 <A HREF=
"#HNR4">Processing energies
</A><br>
101 <A HREF=
"#HNR5">Converting files
</A><br>
102 <A HREF=
"#HNR6">Tools
</A><br>
103 <A HREF=
"#HNR7">Distances between structures
</A><br>
104 <A HREF=
"#HNR8">Distances in structures over time
</A><br>
105 <A HREF=
"#HNR9">Mass distribution properties over time
</A><br>
106 <A HREF=
"#HNR10">Analyzing bonded interactions
</A><br>
107 <A HREF=
"#HNR11">Structural properties
</A><br>
108 <A HREF=
"#HNR12">Kinetic properties
</A><br>
109 <A HREF=
"#HNR13">Electrostatic properties
</A><br>
110 <A HREF=
"#HNR14">Protein specific analysis
</A><br>
111 <A HREF=
"#HNR15">Interfaces
</A><br>
112 <A HREF=
"#HNR16">Covariance analysis
</A><br>
113 <A HREF=
"#HNR17">Normal modes
</A><br>
117 <TABLE CELLSPACING=
1>
118 <TR><TD>
119 <TR><TD COLSPAN=
2><b>Generating topologies and coordinates
</b>
120 <TR><TD><A HREF=
"online/pdb2gmx.html">pdb2gmx
</A><TD>converts pdb files to topology and coordinate files
121 <TR><TD><A HREF=
"online/editconf.html">editconf
</A><TD>edits the box and writes subgroups
122 <TR><TD><A HREF=
"online/genbox.html">genbox
</A><TD>solvates a system
123 <TR><TD><A HREF=
"online/genion.html">genion
</A><TD>generates mono atomic ions on energetically favorable positions
124 <TR><TD><A HREF=
"online/genconf.html">genconf
</A><TD>multiplies a conformation in 'random' orientations
125 <TR><TD><A HREF=
"online/genpr.html">genpr
</A><TD>generates position restraints for index groups
126 <TR><TD><A HREF=
"online/protonate.html">protonate
</A><TD>protonates structures
130 <TABLE CELLSPACING=
1>
131 <TR><TD>
132 <TR><TD COLSPAN=
2><b>Running a simulation
</b>
133 <TR><TD><A HREF=
"online/grompp.html">grompp
</A><TD>makes a run input file
134 <TR><TD><A HREF=
"online/tpbconv.html">tpbconv
</A><TD>makes a run input file for restarting a crashed run
135 <TR><TD><A HREF=
"online/mdrun.html">mdrun
</A><TD>performs a simulation
139 <TABLE CELLSPACING=
1>
140 <TR><TD>
141 <TR><TD COLSPAN=
2><b>Viewing trajectories
</b>
142 <TR><TD><A HREF=
"online/ngmx.html">ngmx
</A><TD>displays a trajectory
143 <TR><TD><A HREF=
"online/trjconv.html">trjconv
</A><TD>converts trajectories to e.g. pdb which can be viewed with e.g. rasmol
147 <TABLE CELLSPACING=
1>
148 <TR><TD>
149 <TR><TD COLSPAN=
2><b>Processing energies
</b>
150 <TR><TD><A HREF=
"online/g_energy.html">g_energy
</A><TD>writes energies to xvg files and displays averages
151 <TR><TD><A HREF=
"online/g_enemat.html">g_enemat
</A><TD>extracts an energy matrix from an energy file
152 <TR><TD><A HREF=
"online/mdrun.html">mdrun
</A><TD>with -rerun (re)calculates energies for trajectory frames
156 <TABLE CELLSPACING=
1>
157 <TR><TD>
158 <TR><TD COLSPAN=
2><b>Converting files
</b>
159 <TR><TD><A HREF=
"online/editconf.html">editconf
</A><TD>converts and manipulates structure files
160 <TR><TD><A HREF=
"online/trjconv.html">trjconv
</A><TD>converts and manipulates trajectory files
161 <TR><TD><A HREF=
"online/trjcat.html">trjcat
</A><TD>concatenates trajectory files
162 <TR><TD><A HREF=
"online/eneconv.html">eneconv
</A><TD>converts energy files
163 <TR><TD><A HREF=
"online/xmp2ps.html">xmp2ps
</A><TD>converts XPM matrices to encapsulated postscript (or XPM)
167 <TABLE CELLSPACING=
1>
168 <TR><TD>
169 <TR><TD COLSPAN=
2><b>Tools
</b>
170 <TR><TD><A HREF=
"online/make_ndx.html">make_ndx
</A><TD>makes index files
171 <TR><TD><A HREF=
"online/mk_angndx.html">mk_angndx
</A><TD>generates index files for g_angle
172 <TR><TD><A HREF=
"online/gmxcheck.html">gmxcheck
</A><TD>checks and compares files
173 <TR><TD><A HREF=
"online/gmxdump.html">gmxdump
</A><TD>makes binary files human readable
174 <TR><TD><A HREF=
"online/g_analyze.html">g_analyze
</A><TD>analyzes data sets
178 <TABLE CELLSPACING=
1>
179 <TR><TD>
180 <TR><TD COLSPAN=
2><b>Distances between structures
</b>
181 <TR><TD><A HREF=
"online/g_rms.html">g_rms
</A><TD>calculates rmsd's with a reference structure and rmsd matrices
182 <TR><TD><A HREF=
"online/g_confrms.html">g_confrms
</A><TD>fits two structures and calculates the rmsd
183 <TR><TD><A HREF=
"online/g_cluster.html">g_cluster
</A><TD>clusters structures
184 <TR><TD><A HREF=
"online/g_rmsf.html">g_rmsf
</A><TD>calculates atomic fluctuations
188 <TABLE CELLSPACING=
1>
189 <TR><TD>
190 <TR><TD COLSPAN=
2><b>Distances in structures over time
</b>
191 <TR><TD><A HREF=
"online/g_mindist.html">g_mindist
</A><TD>calculates the minimum distance between two groups
192 <TR><TD><A HREF=
"online/g_dist.html">g_dist
</A><TD>calculates the distances between the centers of mass of two groups
193 <TR><TD><A HREF=
"online/g_mdmat.html">g_mdmat
</A><TD>calculates residue contact maps
194 <TR><TD><A HREF=
"online/g_rmsdist.html">g_rmsdist
</A><TD>calculates atom pair distances averaged with power
2, -
3 or -
6
198 <TABLE CELLSPACING=
1>
199 <TR><TD>
200 <TR><TD COLSPAN=
2><b>Mass distribution properties over time
</b>
201 <TR><TD><A HREF=
"online/g_com.html">g_com
</A><TD>calculates the center of mass
202 <TR><TD><A HREF=
"online/g_gyrate.html">g_gyrate
</A><TD>calculates the radius of gyration
203 <TR><TD><A HREF=
"online/g_msd.html">g_msd
</A><TD>calculates mean square displacements
204 <TR><TD><A HREF=
"online/g_rotacf.html">g_rotacf
</A><TD>calculates the rotational correlation function for molecules
205 <TR><TD><A HREF=
"online/g_rdf.html">g_rdf
</A><TD>calculates RDF's
206 <TR><TD><A HREF=
"online/g_rdens.html">g_rdens
</A><TD>calculates radial densities
210 <TABLE CELLSPACING=
1>
211 <TR><TD>
212 <TR><TD COLSPAN=
2><b>Analyzing bonded interactions
</b>
213 <TR><TD><A HREF=
"online/g_bond.html">g_bond
</A><TD>calculates bond length distributions
214 <TR><TD><A HREF=
"online/mk_angndx.html">mk_angndx
</A><TD>generates index files for g_angle
215 <TR><TD><A HREF=
"online/g_angle.html">g_angle
</A><TD>calculates distributions and correlations for angles and dihedrals
216 <TR><TD><A HREF=
"online/g_dih.html">g_dih
</A><TD>analyzes dihedral transitions
220 <TABLE CELLSPACING=
1>
221 <TR><TD>
222 <TR><TD COLSPAN=
2><b>Structural properties
</b>
223 <TR><TD><A HREF=
"online/g_hbond.html">g_hbond
</A><TD>computes and analyzes hydrogen bonds
224 <TR><TD><A HREF=
"online/g_saltbr.html">g_saltbr
</A><TD>computes salt bridges
225 <TR><TD><A HREF=
"online/g_sas.html">g_sas
</A><TD>computes solvent accessible surface area
226 <TR><TD><A HREF=
"online/g_order.html">g_order
</A><TD>computes the order parameter per atom for carbon tails
227 <TR><TD><A HREF=
"online/g_sgangle.html">g_sgangle
</A><TD>computes the angle and distance between two groups
228 <TR><TD><A HREF=
"online/g_disre.html">g_disre
</A><TD>analyzes distance restraints
232 <TABLE CELLSPACING=
1>
233 <TR><TD>
234 <TR><TD COLSPAN=
2><b>Kinetic properties
</b>
235 <TR><TD><A HREF=
"online/g_velacc.html">g_velacc
</A><TD>calculates velocity autocorrelation functions
239 <TABLE CELLSPACING=
1>
240 <TR><TD>
241 <TR><TD COLSPAN=
2><b>Electrostatic properties
</b>
242 <TR><TD><A HREF=
"online/genion.html">genion
</A><TD>generates mono atomic ions on energetically favorable positions
243 <TR><TD><A HREF=
"online/g_potential.html">g_potential
</A><TD>calculates the electrostatic potential across the box
244 <TR><TD><A HREF=
"online/g_dipoles.html">g_dipoles
</A><TD>computes the total dipole plus fluctuations
245 <TR><TD><A HREF=
"online/g_dielectric.html">g_dielectric
</A><TD>calculates frequency dependent dielectric constants
249 <TABLE CELLSPACING=
1>
250 <TR><TD>
251 <TR><TD COLSPAN=
2><b>Protein specific analysis
</b>
252 <TR><TD><A HREF=
"online/do_dssp.html">do_dssp
</A><TD>assigns secondary structure and calculates solvent accessible surface area
253 <TR><TD><A HREF=
"online/g_chi.html">g_chi
</A><TD>calculates everything you want to know about chi and other dihedrals
254 <TR><TD><A HREF=
"online/g_helix.html">g_helix
</A><TD>calculates everything you want to know about helices
255 <TR><TD><A HREF=
"online/g_rama.html">g_rama
</A><TD>computes Ramachandran plots
256 <TR><TD><A HREF=
"online/xrama.html">xrama
</A><TD>shows animated Ramachandran plots
257 <TR><TD><A HREF=
"online/wheel.html">wheel
</A><TD>plots helical wheels
261 <TABLE CELLSPACING=
1>
262 <TR><TD>
263 <TR><TD COLSPAN=
2><b>Interfaces
</b>
264 <TR><TD><A HREF=
"online/g_potential.html">g_potential
</A><TD>calculates the electrostatic potential across the box
265 <TR><TD><A HREF=
"online/g_density.html">g_density
</A><TD>calculates the density of the system
266 <TR><TD><A HREF=
"online/g_order.html">g_order
</A><TD>computes the order parameter per atom for carbon tails
267 <TR><TD><A HREF=
"online/g_h2order.html">g_h2order
</A><TD>computes the orientation of water molecules
271 <TABLE CELLSPACING=
1>
272 <TR><TD>
273 <TR><TD COLSPAN=
2><b>Covariance analysis
</b>
274 <TR><TD><A HREF=
"online/g_covar.html">g_covar
</A><TD>calculates and diagonalizes the covariance matrix
275 <TR><TD><A HREF=
"online/g_anaeig.html">g_anaeig
</A><TD>analyzes the eigenvectors
279 <TABLE CELLSPACING=
1>
280 <TR><TD>
281 <TR><TD COLSPAN=
2><b>Normal modes
</b>
282 <TR><TD><A HREF=
"online/grompp.html">grompp
</A><TD>makes a run input file
283 <TR><TD><A HREF=
"online/mdrun.html">mdrun
</A><TD>finds a potential energy minimum
284 <TR><TD><A HREF=
"online/nmrun.html">nmrun
</A><TD>calculates the Hessian
285 <TR><TD><A HREF=
"online/g_nmeig.html">g_nmeig
</A><TD>diagonalizes the Hessian
286 <TR><TD><A HREF=
"online/g_anaeig.html">g_anaeig
</A><TD>analyzes the normal modes
287 <TR><TD><A HREF=
"online/g_nmens.html">g_nmens
</A><TD>generates an ensemble of structures from the normal modes
290 <IMG SRC=
"gif/rainbow.gif" WIDTH=
100% HEIGHT=
7>
