user-guide/cutoff-schemes.rst
user-guide/file-formats.rst
user-guide/tools.rst
+ user-guide/plotje.gif
+ user-guide/xvgr.gif
conf.py
)
set(SPHINX_INPUT_FILES ${SPHINX_CONFIG_VARS_FILE})
.. _webpage: http://www.gromacs.org
.. _ftp site: ftp://ftp.gromacs.org/pub/gromacs/
.. _tutorials: http://www.gromacs.org/Documentation/Tutorials
-.. _sample mdp file: ../online/mdp.html
.. _download: ../download.html
-
-.. _pdb: ../online/pdb.html
-.. _gro: ../online/gro.html
-.. _top: ../online/top.html
-.. _cpt: ../online/cpt.html
-.. _trr: ../online/trr.html
-.. _xtc: ../online/xtc.html
-.. _tng: ../online/tng.html
-.. _tpr: ../online/tpr.html
-.. _ndx: ../online/ndx.html
-.. _mdp: ../online/mdp.html
-.. _log: ../online/log.html
-.. _xvg: ../online/xvg.html
-.. _xpm: ../online/xpm.html
-.. _eps: ../online/eps.html
-.. _edr: ../online/edr.html
-.. _rtp: ../online/rtp.html
""".format(gmx_version_string=gmx_version_string, regressiontest_version=regressiontest_version)
# -- Options for HTML output ----------------------------------------------
+++ /dev/null
-<title>cpt file format</title>
-<h3>Description</h3>
-The cpt file extension stands for portable checkpoint file.
-The complete state of the simulation is stored in the checkpoint file,
-including extended thermostat/barostat variables, random number states
-and NMR time averaged data.
-With domain decomposition also the some decomposition setup information
-is stored.
-<p>
-See also <a href="../programs/gmx-mdrun.html">gmx mdrun</a>.
+++ /dev/null
-<title>dat file format</title>
-<H3>Description</H3>
-Files with the dat file extension contain generic input or output.
-As it is not possible
-to categorise all data file formats, GROMACS has a generic file format called
-dat of which no format is given.
+++ /dev/null
-<title>dlg file format</title>
-<h3>Description</h3>
-The dlg file format is used as input for the
-<a href="../programs/gmx-view.html">gmx view</a>
-trajectory viewer. These files are not meant to be altered by the end user.
-<h3>Sample</h3>
-<pre>
-grid 39 18 {
-
-group "Bond Options" 1 1 16 9 {
- radiobuttons { " Thin Bonds" " Fat Bonds" " Very Fat Bonds" " Spheres" }
- "bonds" "Ok" " F" "help bonds"
-}
-
-group "Other Options" 18 1 20 13 {
- checkbox " Show Hydrogens" "" "" "FALSE" "help opts"
- checkbox " Draw plus for atoms" "" "" "TRUE" "help opts"
- checkbox " Show Box" "" "" "TRUE" "help opts"
- checkbox " Remove PBC" "" "" "FALSE" "help opts"
- checkbox " Depth Cueing" "" "" "TRUE" "help opts"
- edittext "Skip frames: " "" "" "0" "help opts"
-}
-
-simple 1 15 37 2 {
- defbutton "Ok" "Ok" "Ok" "Ok" "help bonds"
-}
-
-}
-</pre>
+++ /dev/null
-<title>edi file format</title>
-<h3>Description</h3>
-Files with the edi file extension contain information for
-<a href="../programs/gmx-mdrun.html">gmx mdrun</a>
-to run Molecular Dynamics with Essential Dynamics constraints.
-<!-- WEDSAM and ESSDYN seem to have vanished from WhatIf and the web-->
-<!--These files can be generated by the program <tt>WEDSAM</tt> which uses
-output from the programs in the <tt>ESSDYN</tt> menu of the
-<A HREF="http://www.sander.embl-heidelberg.de/whatif/">WHAT IF</A> program.-->
+++ /dev/null
-<title>edo file format</title>
-<h3>Description</h3>
-Files with the edo file extension are generated by
-<a href="../programs/gmx-mdrun.html">gmx mdrun</a>
-if Molecular Dynamics is performed with Essential Dynamics
-constraints. Depending on the parameters set in the <a href="edi.html">
-edi</a> file, edo files may contain projections of positions,
-velocities and forces onto selected eigenvectors during the run as well
-as RMSD values, or information about specific types of constraints.
-Specific results can be extracted from the edo files with standard unix
-utilities like <tt>awk</tt>.
+++ /dev/null
-<title>ene file format</title>
-<h3>Description</h3>
-The edr file extension stands for portable energy file.
-The energies are stored using the xdr protocol.
-<p>
-See also <a href="../programs/gmx-energy.html">gmx energy</a>.
+++ /dev/null
-<title>ene file format</title>
-<h3>Description</h3>
-The ene file extension stands for binary energy file. It holds the
-energies as generated during your
-<a href="../programs/gmx-mdrun.html">gmx mdrun</a>.
-<br>
-The file can be transformed to a portable energy file (portable
-accross hardware platforms), the
-<a href="edr.html">.edr</a> file using the program
-<a href="../programs/gmx-eneconv.html">gmx eneconv</a>.
-<p>
-See also <a href="../programs/gmx-energy.html">gmx energy</a>.
+++ /dev/null
-<title>eps file format</title>
-<H3>Description</H3>
-The eps file format is not a special GROMACS format, but just a
-variant of the standard PostScript(tm). A sample eps file as
-generated by the <a href="../programs/gmx-xpm2ps.html">gmx xpm2ps</a> program is
-included below. It shows the secondary structure of a peptide as a function
-of time.
-<p>
-<img src="../images/plotje.gif" alt="hallo">
+++ /dev/null
-<TITLE>File formats</TITLE>
-<dl>
-<dt><h3>Parameter files</h3>
-<dl compact>
-<a href="mdp.html">mdp</a>
-<dd>run parameters, input for
-<a href="../programs/gmx-grompp.html">gmx grompp</a> and
-<a href="../programs/gmx-convert-tpr.html">gmx convert-tpr</a>
-<dt><a href="m2p.html">m2p</a>
-<dd>input for <a href="../programs/gmx-xpm2ps.html">gmx xpm2ps</a>
-</dl>
-
-<br><dt><h3>Structure files</h3>
-<dd> <dl compact>
-<dt><a href="gro.html">gro</a> <dd>GROMACS format
-<dt><a href="g96.html">g96</a> <dd>GROMOS-96 format
-<dt><a href="pdb.html">pdb</a> <dd>brookhaven Protein DataBank format
-<dt><b>Generic structure formats:</b>
-<a href="gro.html">gro</a>,
-<a href="g96.html">g96</a>,
-<a href="pdb.html">pdb</a>, or
-<a href="tpr.html">tpr</a>
-<dt><b>Structure+mass(db):</b>
-<a href="tpr.html">tpr</a>,
-<a href="gro.html">gro</a>,
-<a href="g96.html">g96</a> or
-<a href="pdb.html">pdb</a>.
-<dd>Structure and mass input for analysis tools.
-When gro or pdb is used approximate masses will be read from the mass database.
-</dl>
-
-<br><dt><h3>Topology files</h3>
-<dd><dl compact>
-<dt><a href="top.html">top</a> <dd>system topology (ascii)
-<dt><a href="itp.html">itp</a> <dd>include topology (ascii)
-<dt><a href="rtp.html">rtp</a> <dd>residue topology (ascii)
-<dt><a href="ndx.html">ndx</a> <dd>index file
-</dl>
-
-<br><dt><h3>Run Input files</h3>
-<dd><dl compact>
-<dt><a href="tpr.html">tpr</a> <dd>system topology, parameters, coordinates
-and velocities (binary, portable)
-<dt><b>Generic run input file formats:</b>
-<a href="tpr.html">tpr</a>
-
-</dl>
-
-<br><dt><h3>Trajectory files</h3>
-<dd><dl compact>
-<dt><a href="tng.html">tng</a> <dd>Any kind of data (compressed, portable, any precision)
-<dt><a href="trr.html">trr</a> <dd>x, v and f (binary, full precision, portable)
-<dt><a href="xtc.html">xtc</a> <dd>x only (compressed, portable, any precision)
-<dt><a href="gro.html">gro</a> <dd>x and v (ascii, any precision)
-<dt><a href="g96.html">g96</a> <dd>x only (ascii, fixed high precision)
-<dt><a href="pdb.html">pdb</a> <dd>x only (ascii, reduced precision)
-<dt><b>Formats for full-precision data:</b>
-<a href="tng.html">tng</a> or
-<a href="trr.html">trr</a>
-<dt><b>Generic trajectory formats:</b>
-<a href="tng.html">tng</a>,
-<a href="xtc.html">xtc</a>,
-<a href="trr.html">trr</a>,
-<a href="gro.html">gro</a>,
-<a href="g96.html">g96</a>,
-<a href="pdb.html">pdb</a> or
-</dl>
-
-<br><dt><h3>Energy files</h3>
-<dd><dl compact>
-<dt><a href="ene.html">ene</a> <dd>energies, temperature, pressure, box size,
-density and virials (binary)
-<dt><a href="edr.html">edr</a> <dd>energies, temperature, pressure, box size,
-density and virials (binary, portable)
-<dt><b>Generic energy formats:</b>
-<a href="edr.html">edr</a> or
-<a href="ene.html">ene</a>
-</dl>
-
-<br><dt><h3>Other files</h3>
-<dd><dl compact>
-<dt><a href="dat.html">dat</a> <dd>generic, preferred for input
-<dt><a href="edi.html">edi</a>
-<dd>essential dynamics constraints input for
-<a href="../programs/gmx-mdrun.html">gmx mdrun</a>
-<dt><a href="edo.html">edo</a>
-<dd>essential dynamics constraints output for
-<a href="../programs/gmx-mdrun.html">gmx mdrun</a>
-<dt><a href="eps.html">eps</a> <dd>Encapsulated Postscript
-<dt><a href="log.html">log</a> <dd>log file
-<dt><a href="map.html">map</a> <dd>colormap input for
-<a href="../programs/gmx-do_dssp.html">gmx do_dssp</a>
-<dt><a href="mtx.html">mtx</a> <dd>binary matrix data
-<dt><a href="out.html">out</a> <dd>generic, preferred for output
-<dt><a href="tex.html">tex</a> <dd>LaTeX input
-<dt><a href="xpm.html">xpm</a> <dd>ascii matrix data, use
-<a href="../programs/gmx-xpm2ps.html">gmx xpm2ps</A> to convert to <a href="eps.html">eps</a>
-<dt><a href="xvg.html">xvg</a> <dd>xvgr input
-</dl>
-</dl>
+++ /dev/null
-<title>g96 file format</title>
-<h3>Description</h3>
-<p>A file with the g96 extension can be a GROMOS-96 initial/final
-configuration file or a coordinate trajectory file or a combination of both.
-The file is fixed format, all floats are written as 15.9 (files can get huge).
-GROMACS supports the following data blocks in the given order:
-<ul>
-<li> Header block:
-<ul>
-<li><tt>TITLE</tt> (mandatory)
-</ul>
-<li> Frame blocks:
-<ul>
-<li><tt>TIMESTEP</tt> (optional)
-<li><tt>POSITION/POSITIONRED</tt> (mandatory)
-<li><tt>VELOCITY/VELOCITYRED</tt> (optional)
-<li><tt>BOX</tt> (optional)
-</ul>
-</ul>
-See the GROMOS-96 manual for a complete description of the blocks.
-<p>
-Note that all GROMACS programs can read compressed or g-zipped files.
+++ /dev/null
-<title>gro file format</title>
-<h3>Description</h3>
-<p>Files with the gro file extension contain a molecular structure in
-Gromos87 format. gro files can be used as trajectory by simply
-concatenating files. An attempt will be made to read a time value from
-the title string in each frame, which should be preceded by
-'<TT>t=</TT>', as in the sample below.</p>
-
-<p>A sample piece is included below:
-<pre>
-MD of 2 waters, t= 0.0
- 6
- 1WATER OW1 1 0.126 1.624 1.679 0.1227 -0.0580 0.0434
- 1WATER HW2 2 0.190 1.661 1.747 0.8085 0.3191 -0.7791
- 1WATER HW3 3 0.177 1.568 1.613 -0.9045 -2.6469 1.3180
- 2WATER OW1 4 1.275 0.053 0.622 0.2519 0.3140 -0.1734
- 2WATER HW2 5 1.337 0.002 0.680 -1.0641 -1.1349 0.0257
- 2WATER HW3 6 1.326 0.120 0.568 1.9427 -0.8216 -0.0244
- 1.82060 1.82060 1.82060
-</pre>
-
-Lines contain the following information (top to bottom):
-<ul>
-<li>title string (free format string, optional time in ps after '<TT>t=</TT>')
-<li>number of atoms (free format integer)
-<li>one line for each atom (fixed format, see below)
-<li>box vectors (free format, space separated reals), values: v1(x) v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y),
-the last 6 values may be omitted (they will be set to zero).
-Gromacs only supports boxes with v1(y)=v1(z)=v2(z)=0.
-
-
-</ul>
-
-This format is fixed, ie. all columns are in a fixed
-position. Optionally (for now only yet with trjconv) you can write gro
-files with any number of decimal places, the format will then be
-<tt>n+5</tt> positions with <tt>n</tt> decimal places (<tt>n+1</tt>
-for velocities) in stead of <tt>8</tt> with <tt>3</tt> (with
-<tt>4</tt> for velocities). Upon reading, the precision will be
-inferred from the distance between the decimal points (which will be
-<tt>n+5</tt>). Columns contain the following information (from left to
-right):
-
-<ul>
-<li>residue number (5 positions, integer)
-<li>residue name (5 characters)
-<li>atom name (5 characters)
-<li>atom number (5 positions, integer)
-<li>position (in nm, x y z in 3 columns, each 8 positions with 3
-decimal places)
-<li>velocity (in nm/ps (or km/s), x y z in 3 columns, each 8 positions with 4
-decimal places)
-</ul>
-
-Note that separate molecules or ions (e.g. water or Cl-) are regarded
-as residues. If you want to write such a file in your own program
-without using the GROMACS libraries you can use the following formats:
-
-<dl>
-<dt>C format
-<dd><tt>"%5d%-5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f"</tt>
-<dt>Fortran format
-<dd><tt>(i5,2a5,i5,3f8.3,3f8.4)</tt>
-<dt>Pascal format
-<dd>This is left as an exercise for the user
-</dl>
-Note that this is the format for writing, as in the above example
-fields may be written without spaces, and therefore can not be read
-with the same format statement in C.
+++ /dev/null
-<title>hdb file format</title>
-<H3>Description</H3>
-The hdb file extension stands for hydrogen database
-Such a file is needed by <a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a>
-when building hydrogen atoms that were either originally missing, or that
-were removed with <tt>-ignh</tt>.
-</PRE>
+++ /dev/null
-<title>itp file format</title>
-<h3>Description</h3>
-The itp file extension stands for include toplogy. These files are included in topology files ( with the <a href="top.html"><tt>top</tt></a> extension )
+++ /dev/null
-<title>log file format</title>
-<h3>Description</h3>
-Logfiles are generated by some GROMACS programs and are usually in
-human-readable format. Use <tt>more logfile</tt>.
+++ /dev/null
-<title>m2p file format</title>
-<h3>Description</h3>
-The m2p file format contains input options for the
-<a href="../programs/gmx-xpm2ps.html">gmx xpm2ps</a> program. All of these options
-are very easy to comprehend when you look at the PosScript(tm) output
-from <a href="../programs/gmx-xpm2ps.html">gmx xpm2ps</a>.
-<pre>
-; Command line options of xpm2ps override the parameters in this file
-black&white = no ; Obsolete
-titlefont = Times-Roman ; A PostScript Font
-titlefontsize = 20 ; Font size (pt)
-legend = yes ; Show the legend
-legendfont = Times-Roman ; A PostScript Font
-legendlabel = ; Used when there is none in the .xpm
-legend2label = ; Used when merging two xpm's
-legendfontsize = 14 ; Font size (pt)
-xbox = 2.0 ; x-size of a matrix element
-ybox = 2.0 ; y-size of a matrix element
-matrixspacing = 20.0 ; Space between 2 matrices
-xoffset = 0.0 ; Between matrix and bounding box
-yoffset = 0.0 ; Between matrix and bounding box
-x-major = 20 ; Major ticks on x axis every .. frames
-x-minor = 5 ; Id. Minor ticks
-x-firstmajor = 0 ; First frame for major tick
-x-majorat0 = no ; Major tick at first frame
-x-majorticklen = 8.0 ; x-majorticklength
-x-minorticklen = 4.0 ; x-minorticklength
-x-label = ; Used when there is none in the .xpm
-x-fontsize = 16 ; Font size (pt)
-x-font = Times-Roman ; A PostScript Font
-x-tickfontsize = 10 ; Font size (pt)
-x-tickfont = Helvetica ; A PostScript Font
-y-major = 20
-y-minor = 5
-y-firstmajor = 0
-y-majorat0 = no
-y-majorticklen = 8.0
-y-minorticklen = 4.0
-y-label =
-y-fontsize = 16
-y-font = Times-Roman
-y-tickfontsize = 10
-y-tickfont = Helvetica
-</pre>
+++ /dev/null
-<title>map file format</title>
-<H3>Description</H3>
-This file maps matrix data to RGB values which is used by the
-<a href="../programs/gmx-do_dssp.html">gmx do_dssp</a> program.<p>
-The format of this file is as follow: first line number of elements
-in the colormap. Then for each line: The first character is
-a code for the secondary structure type.
-Then comes a string for use in the legend of the plot and then the
-R (red) G (green) and B (blue) values. <p>
-In this case the colors are
-(in order of appearance): white, red, black, cyan, yellow, blue,
-magenta, orange.
-<pre>
-8
-~ Coil 1.0 1.0 1.0
-E B-Sheet 1.0 0.0 0.0
-B B-Bridge 0.0 0.0 0.0
-S Bend 0.0 0.8 0.8
-T Turn 1.0 1.0 0.0
-H A-Helix 0.0 0.0 1.0
-G 3-Helix 1.0 0.0 1.0
-I 5-Helix 1.0 0.6 0.0
-</pre>
+++ /dev/null
-<title>mdp file format</title>
-<P> See the user guide
-for a detailed description of the options</a>. </P>
-
-<P> Below is a sample mdp file.
-The ordering of the items is not important, but if you enter the same
-thing twice, the <b>last</b> is used (grompp gives you a note when
-overriding values). Dashes and underscores on the
-left hand side are ignored.</P>
-
-<P> The values of the options are reasonable values for a 1 nanosecond
-MD run of a protein in a box of water. </P>
-
-<hr>
-<pre>
-title = Yo
-cpp = /lib/cpp
-include = -I../top
-define =
-integrator = md
-dt = 0.002
-nsteps = 500000
-nstxout = 5000
-nstvout = 5000
-nstlog = 5000
-nstenergy = 250
-nstxout-compressed = 250
-compressed-x-grps = Protein
-energygrps = Protein SOL
-nstlist = 10
-ns-type = grid
-rlist = 0.8
-coulombtype = cut-off
-rcoulomb = 1.4
-rvdw = 0.8
-tcoupl = Berendsen
-tc-grps = Protein SOL
-tau-t = 0.1 0.1
-ref-t = 300 300
-Pcoupl = Berendsen
-tau-p = 1.0
-compressibility = 4.5e-5
-ref-p = 1.0
-gen-vel = yes
-gen-temp = 300
-gen-seed = 173529
-constraints = all-bonds
-</pre>
-<hr>
-
-<p>
-With this input <a href="../programs/gmx-grompp.html"><tt>grompp</tt></a> will produce
-an <tt>mdout.mdp</tt> with all the options and descriptions:
-</p>
-
-<hr>
-<pre>
-; VARIOUS PREPROCESSING OPTIONS =
-title = Yo
-cpp = /lib/cpp
-include = -I../top
-define =
-
-; RUN CONTROL PARAMETERS =
-integrator = md
-; start time and timestep in ps =
-tinit = 0
-dt = 0.002
-nsteps = 500000
-; number of steps for center of mass motion removal =
-nstcomm = 1
-comm-grps =
-
-; LANGEVIN DYNAMICS OPTIONS =
-; Temperature, friction coefficient (amu/ps) and random seed =
-bd-temp = 300
-bd-fric = 0
-ld-seed = 1993
-
-; ENERGY MINIMIZATION OPTIONS =
-; Force tolerance and initial step-size =
-emtol = 100
-emstep = 0.01
-; Max number of iterations in relax-shells =
-niter = 20
-; Frequency of steepest descents steps when doing CG =
-nstcgsteep = 1000
-
-; OUTPUT CONTROL OPTIONS =
-; Output frequency for coords (x), velocities (v) and forces (f) =
-nstxout = 5000
-nstvout = 5000
-nstfout = 0
-; Output frequency for energies to log file and energy file =
-nstlog = 5000
-nstenergy = 250
-; Output frequency and precision for xtc file =
-nstxout-compressed = 250
-compressed-x-precision = 1000
-; This selects the subset of atoms for the xtc file. You can =
-; select multiple groups. By default all atoms will be written. =
-compressed-x-grps = Protein
-; Selection of energy groups =
-energygrps = Protein SOL
-
-; NEIGHBORSEARCHING PARAMETERS =
-; nblist update frequency =
-nstlist = 10
-; ns algorithm (simple or grid) =
-ns-type = grid
-; Periodic boundary conditions: xyz or none =
-pbc = xyz
-; nblist cut-off =
-rlist = 0.8
-
-; OPTIONS FOR ELECTROSTATICS AND VDW =
-; Method for doing electrostatics =
-coulombtype = cut-off
-rcoulomb-switch = 0
-rcoulomb = 1.4
-; Dielectric constant (DC) for cut-off or DC of reaction field =
-epsilon-r = 1
-; Method for doing Van der Waals =
-vdw-type = Cut-off
-; cut-off lengths =
-rvdw-switch = 0
-rvdw = 0.8
-; Apply long range dispersion corrections for Energy and Pressure =
-DispCorr = No
-; Spacing for the PME/PPPM FFT grid =
-fourierspacing = 0.12
-; FFT grid size, when a value is 0 fourierspacing will be used =
-fourier-nx = 0
-fourier-ny = 0
-fourier-nz = 0
-; EWALD/PME/PPPM parameters =
-pme-order = 4
-ewald-rtol = 1e-05
-epsilon-surface = 0
-
-; OPTIONS FOR WEAK COUPLING ALGORITHMS =
-; Temperature coupling =
-tcoupl = Berendsen
-; Groups to couple separately =
-tc-grps = Protein SOL
-; Time constant (ps) and reference temperature (K) =
-tau-t = 0.1 0.1
-ref-t = 300 300
-; Pressure coupling =
-Pcoupl = Berendsen
-Pcoupltype = Isotropic
-; Time constant (ps), compressibility (1/bar) and reference P (bar) =
-tau-p = 1.0
-compressibility = 4.5e-5
-ref-p = 1.0
-
-; SIMULATED ANNEALING CONTROL =
-annealing = no
-; Time at which temperature should be zero (ps) =
-zero-temp-time = 0
-
-; GENERATE VELOCITIES FOR STARTUP RUN =
-gen-vel = yes
-gen-temp = 300
-gen-seed = 173529
-
-; OPTIONS FOR BONDS =
-constraints = all-bonds
-; Type of constraint algorithm =
-constraint-algorithm = Lincs
-; Do not constrain the start configuration =
-unconstrained-start = no
-; Relative tolerance of shake =
-shake-tol = 0.0001
-; Highest order in the expansion of the constraint coupling matrix =
-lincs-order = 4
-; Lincs will write a warning to the stderr if in one step a bond =
-; rotates over more degrees than =
-lincs-warnangle = 30
-; Convert harmonic bonds to morse potentials =
-morse = no
-
-; NMR refinement stuff =
-; Distance restraints type: No, Simple or Ensemble =
-disre = No
-; Force weighting of pairs in one distance restraint: Equal or Conservative =
-disre-weighting = Equal
-; Use sqrt of the time averaged times the instantaneous violation =
-disre-mixed = no
-disre-fc = 1000
-disre-tau = 0
-; Output frequency for pair distances to energy file =
-nstdisreout = 100
-
-; Free energy control stuff =
-free-energy = no
-init-lambda = 0
-delta-lambda = 0
-sc-alpha = 0
-sc-sigma = 0.3
-
-; Non-equilibrium MD stuff =
-acc-grps =
-accelerate =
-freezegrps =
-freezedim =
-cos-acceleration = 0
-energygrp-excl =
-
-; Electric fields =
-; Format is number of terms (int) and for all terms an amplitude (real) =
-; and a phase angle (real) =
-E-x =
-E-xt =
-E-y =
-E-yt =
-E-z =
-E-zt =
-
-; User defined thingies =
-user1-grps =
-user2-grps =
-userint1 = 0
-userint2 = 0
-userint3 = 0
-userint4 = 0
-userreal1 = 0
-userreal2 = 0
-userreal3 = 0
-userreal4 = 0
-</pre>
+++ /dev/null
-<title>mtx file format</title>
-<H3>Description</H3>
-Files with the mtx file extension contain a matrix.
-The file format is identical to the <a href="trr.html">trr</a> format.
-Currently this file format is only used for hessian matrices,
-which are produced with <a href="../programs/gmx-mdrun.html">gmx mdrun</a> and read by
-<a href="../programs/gmx-nmeig.html">gmx nmeig</a>.
+++ /dev/null
-<title>ndx file format</title>
-<H3>Description</H3>
-The GROMACS index file (usually called index.ndx) contains some
-user definable sets of atoms. The file can be read by
-most analysis programs, by the graphics program
-(<a href="../programs/gmx-view.html">gmx view</a>)
-and by the preprocessor (<a href="../programs/gmx-grompp.html">gmx grompp</a>).
-Most of these programs create default index groups when no index
-file is supplied, so you only need to make an index file when you need special
-groups.
-<p>
-First the group name is written between square brackets.
-The following atom numbers may be spread out over as many lines as you like.
-The atom numbering starts at 1.
-<p>
-
-An example file is here:
-<pre>
-[ Oxygen ]
-1 4 7
-[ Hydrogen ]
-2 3 5 6
-8 9
-</pre>
-
-There are two groups, and total nine atoms. The first group
-<b>Oxygen</b> has 3 elements.
-The second group <b>Hydrogen</b> has 6 elements.
-<p>
-An index file generation tool is available:
-<a href="../programs/gmx-make_ndx.html">gmx make_ndx</a>.
+++ /dev/null
-<title>out file format</title>
-<H3>Description</H3>
-Files with the out file extension contain generic output. As it is not possible
-to categorise all data file formats, GROMACS has a generic file format called
-out of which no format is given.
+++ /dev/null
-<title>pdb file format</title>
-<H3>Description</H3>
-
-Files with the <a href="pdb.html">.pdb</a> extension are molecular
-structure files in the protein databank file format. The protein
-databank file format describes the positions of atoms in a molecular
-structure. Coordinates are read from the ATOM and HETATM records,
-until the file ends or an ENDMDL record is encountered.
-GROMACS programs can read and write a simlation box in the
-CRYST1 entry.
-The pdb format can also be used as a trajectory format:
-several structures, seperated by ENDMDL, can be read from
-or written to one file.
-
-<p>
-<h2>Example</h2>
-An pdb file should look like this
-<PRE>
-ATOM 1 H1 LYS 1 14.260 6.590 34.480 1.00 0.00
-ATOM 2 H2 LYS 1 13.760 5.000 34.340 1.00 0.00
-ATOM 3 N LYS 1 14.090 5.850 33.800 1.00 0.00
-ATOM 4 H3 LYS 1 14.920 5.560 33.270 1.00 0.00
-...
-...
-</PRE>
+++ /dev/null
-<title>rtp file format</title>
-<H3>Description</H3>
-The rtp file extension stands for residue toplogy.
-Such a file is needed by <a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a>
-to make a GROMACS topology for a protein contained in a <tt>.pdb</tt>
-file. The file contains the default interaction type for the 4 bonded
-interactions and residue entries, which consist of atoms and
-optionally bonds, angles dihedrals and impropers.
-Parameters can be added to bonds, angles, dihedrals and impropers,
-these parameters override the standard parameters
-in the <a href="itp.html"><tt>.itp</tt></a> files.
-This should only be used in special cases.
-Instead of parameters a string can be added for each bonded interaction,
-the string is copied to the <a href="top.html"><tt>.top</tt></a> file,
-this is used for the GROMOS96 forcefield.
-<p>
-<a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a>
-automatically generates all angles,
-this means that the <tt>[angles]</tt> field is only
-useful for overriding <a href="itp.html"><tt>.itp</tt></a> parameters.
-<p>
-<a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a>
-automatically generates one proper
-dihedral for every rotatable bond, preferably on heavy atoms.
-When the <tt>[dihedrals]</tt> field is used, no other dihedrals will
-be generated for the bonds corresponding to the specified dihedrals.
-It is possible to put more than one dihedral on a rotatable bond.
-<p>
-<a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a>
-sets the number exclusions to 3, which
-means that interactions between atoms connected by at most 3 bonds are
-excluded. Pair interactions are generated for all pairs of atoms which are
-seperated by 3 bonds (except pairs of hydrogens).
-When more interactions need to be excluded, or some pair interactions should
-not be generated, an <tt>[exclusions]</tt> field can be added, followed by
-pairs of atom names on seperate lines. All non-bonded and pair interactions
-between these atoms will be excluded.
-<p>
-A sample is included below.
-
-
-<PRE>
-[ bondedtypes ] ; mandatory
-; bonds angles dihedrals impropers
- 1 1 1 2 ; mandatory
-
-[ GLY ] ; mandatory
-
- [ atoms ] ; mandatory
-; name type charge chargegroup
- N N -0.280 0
- H H 0.280 0
- CA CH2 0.000 1
- C C 0.380 2
- O O -0.380 2
-
- [ bonds ] ; optional
-;atom1 atom2 b0 kb
- N H
- N CA
- CA C
- C O
- -C N
-
- [ exclusions ] ; optional
-;atom1 atom2
-
- [ angles ] ; optional
-;atom1 atom2 atom3 th0 cth
-
- [ dihedrals ] ; optional
-;atom1 atom2 atom3 atom4 phi0 cp mult
-
- [ impropers ] ; optional
-;atom1 atom2 atom3 atom4 q0 cq
- N -C CA H
- -C -CA N -O
-
-
-[ ZN ]
- [ atoms ]
- ZN ZN 2.000 0
-</PRE>
+++ /dev/null
-<title>tex file format</title>
-<H3>Description</H3>
-We use <b>LaTeX</b> for <i>document</i> processing.
-Although the input is not so
-user friendly, it has some advantages over <i>word</i> processors.
-<ul>
-<li> <b>LaTeX</b> knows a lot about formatting, probably much more than you.
-<li> The input is clear, you always know what you are doing
-<li> It makes anything from letters to a thesis
-<li> Much more...
-</ul>
+++ /dev/null
-<title>tng file format</title>
-<h3>Description</h3>
-Files with the .tng file extension can contain all kinds of data
-related to the trajectory of a simulation. For example, it might
-contain coordinates, velocities, forces and/or energies. Various .mdp
-file options control which of these are written by mdrun, whether data
-is written with compression, and how lossy that compression can be.
-This file is in portable binary format an can be read
-with <a href="../programs/gmx-dump.html">gmx dump</a>.
-<PRE>
-% <a href="../programs/gmx-dump.html">gmx dump</a> -f traj.tng
-</PRE>
-or if you're not such a fast reader:
-<PRE>
-% gmxdump -f traj.tng | more
-</PRE>
-
-<p>
-You can also get a quick look in the contents of the file (number of
-frames etc.) using:
-<PRE>
-% <a href="../programs/gmx-check.html">gmx check</a> -f traj.tng
-</PRE>
+++ /dev/null
-<title>top file format</title>
-<H3>Description</H3>
-The top file extension stands for topology. It is an ascii file which is
-read by <a href="../programs/gmx-grompp.html">gmx grompp</a> which processes it
-and creates a binary topology (<a href="tpr.html">.tpr file</a>).<br>
-A sample file is included below:
-<pre>
-;
-; Example topology file
-;
-[ defaults ]
-; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
- 1 1 no 1.0 1.0
-
-; The force field files to be included
-#include "rt41c5.itp"
-
-[ moleculetype ]
-; name nrexcl
-Urea 3
-
-[ atoms ]
-; nr type resnr residu atom cgnr charge
- 1 C 1 UREA C1 1 0.683
- 2 O 1 UREA O2 1 -0.683
- 3 NT 1 UREA N3 2 -0.622
- 4 H 1 UREA H4 2 0.346
- 5 H 1 UREA H5 2 0.276
- 6 NT 1 UREA N6 3 -0.622
- 7 H 1 UREA H7 3 0.346
- 8 H 1 UREA H8 3 0.276
-
-[ bonds ]
-; ai aj funct c0 c1
- 3 4 1 1.000000e-01 3.744680e+05
- 3 5 1 1.000000e-01 3.744680e+05
- 6 7 1 1.000000e-01 3.744680e+05
- 6 8 1 1.000000e-01 3.744680e+05
- 1 2 1 1.230000e-01 5.020800e+05
- 1 3 1 1.330000e-01 3.765600e+05
- 1 6 1 1.330000e-01 3.765600e+05
-
-[ pairs ]
-; ai aj funct c0 c1
- 2 4 1 0.000000e+00 0.000000e+00
- 2 5 1 0.000000e+00 0.000000e+00
- 2 7 1 0.000000e+00 0.000000e+00
- 2 8 1 0.000000e+00 0.000000e+00
- 3 7 1 0.000000e+00 0.000000e+00
- 3 8 1 0.000000e+00 0.000000e+00
- 4 6 1 0.000000e+00 0.000000e+00
- 5 6 1 0.000000e+00 0.000000e+00
-
-[ angles ]
-; ai aj ak funct c0 c1
- 1 3 4 1 1.200000e+02 2.928800e+02
- 1 3 5 1 1.200000e+02 2.928800e+02
- 4 3 5 1 1.200000e+02 3.347200e+02
- 1 6 7 1 1.200000e+02 2.928800e+02
- 1 6 8 1 1.200000e+02 2.928800e+02
- 7 6 8 1 1.200000e+02 3.347200e+02
- 2 1 3 1 1.215000e+02 5.020800e+02
- 2 1 6 1 1.215000e+02 5.020800e+02
- 3 1 6 1 1.170000e+02 5.020800e+02
-
-[ dihedrals ]
-; ai aj ak al funct c0 c1 c2
- 2 1 3 4 1 1.800000e+02 3.347200e+01 2.000000e+00
- 6 1 3 4 1 1.800000e+02 3.347200e+01 2.000000e+00
- 2 1 3 5 1 1.800000e+02 3.347200e+01 2.000000e+00
- 6 1 3 5 1 1.800000e+02 3.347200e+01 2.000000e+00
- 2 1 6 7 1 1.800000e+02 3.347200e+01 2.000000e+00
- 3 1 6 7 1 1.800000e+02 3.347200e+01 2.000000e+00
- 2 1 6 8 1 1.800000e+02 3.347200e+01 2.000000e+00
- 3 1 6 8 1 1.800000e+02 3.347200e+01 2.000000e+00
-
-[ dihedrals ]
-; ai aj ak al funct c0 c1
- 3 4 5 1 2 0.000000e+00 1.673600e+02
- 6 7 8 1 2 0.000000e+00 1.673600e+02
- 1 3 6 2 2 0.000000e+00 1.673600e+02
-
-; Include SPC water topology
-#include "spc.itp"
-
-[ system ]
-Urea in Water
-
-[ molecules ]
-Urea 1
-SOL 1000
-</pre>
+++ /dev/null
-<title>tpr file format</title>
-<h3>Description</h3>
-The tpr file extension stands for portable binary run input file. This file
-contains the starting structure of your simulation, the molecular topology
-and all the simulation parameters. Because this file is in binary format it
-cannot be read with a normal editor. To read a portable binary run input
-file type:
-<PRE>
-% <a href="../programs/gmx-dump.html">gmx dump</a> -s topol.tpr
-</PRE>
-or if you're not such a fast reader:
-<PRE>
-% gmxdump -s topol.tpr | more
-</PRE>
-
-<p>
-You can also compare two tpr files using:
-<pre>
-% <a href="../programs/gmx-check.html">gmx check</a> -s1 top1 -s2 top2 | more
-</pre>
+++ /dev/null
-<title>trr file format</title>
-<h3>Description</h3>
-Files with the trr file extension contain the trajectory of a simulation.
-In this file all the coordinates, velocities, forces and energies are
-printed as you told GROMACS in your mdp file. This file is in portable binary
-format an can be read with <a href="../programs/gmx-dump.html">gmx dump</a>.
-<PRE>
-% <a href="../programs/gmx-dump.html">gmx dump</a> -f traj.trr
-</PRE>
-or if you're not such a fast reader:
-<PRE>
-% gmxdump -f traj.trr | more
-</PRE>
-
-<p>
-You can also get a quick look in the contents of the file (number of
-frames etc.) using:
-<PRE>
-% <a href="../programs/gmx-check.html">gmx check</a> -f traj.trr
-</PRE>
+++ /dev/null
-<title>xpm file format</title>
-<H3>Description</H3>
-The GROMACS xpm file format is compatible with the XPixMap format
-and is used for storing matrix data.
-Thus GROMACS xpm files can be viewed directly with programs like XV.
-Alternatively, they can be imported into GIMP and scaled to 300 DPI,
-using strong antialiasing for font and graphics.
-The first matrix data line in an xpm file corresponds to the last matrix
-row.
-In addition to the XPixMap format, GROMACS xpm files may contain
-extra fields. The information in these fields is used when converting
-an xpm file to EPS with
-<A HREF="../programs/gmx-xpm2ps.html">gmx xpm2ps</a>.
-The optional extra field are:
-<ul>
-<li>
-Before the <tt>gv_xpm</tt> declaration: <tt>title</tt>, <tt>legend</tt>,
-<tt>x-label</tt>, <tt>y-label</tt> and <tt>type</tt>,
-all followed by a string.
-The <tt>legend</tt> field determines the legend title.
-The <tt>type</tt> field must be followed by <tt>"continuous"</tt> or
-<tt>"discrete"</tt>,
-this determines which type of legend will be drawn in an EPS file,
-the default type is continuous.
-<li>
-The xpm colormap entries may be followed by a string, which is a label for
-that color.
-<li>
-Between the colormap and the matrix data, the fields
-<tt>x-axis</tt> and/or <tt>y-axis</tt>
-may be present followed by the tick-marks for that axis.
-</ul>
-The example GROMACS xpm file below contains all the extra fields.
-The C-comment delimiters and the colon in the extra fields are optional.
-<pre>
-/* XPM */
-/* This matrix is generated by g_rms. */
-/* title: "Backbone RMSD matrix" */
-/* legend: "RMSD (nm)" */
-/* x-label: "Time (ps)" */
-/* y-label: "Time (ps)" */
-/* type: "Continuous" */
-static char * gv_xpm[] = {
-"13 13 6 1",
-"A c #FFFFFF " /* "0" */,
-"B c #CCCCCC " /* "0.0399" */,
-"C c #999999 " /* "0.0798" */,
-"D c #666666 " /* "0.12" */,
-"E c #333333 " /* "0.16" */,
-"F c #000000 " /* "0.2" */,
-/* x-axis: 0 40 80 120 160 200 240 280 320 360 400 440 480 */
-/* y-axis: 0 40 80 120 160 200 240 280 320 360 400 440 480 */
-"FEDDDDCCCCCBA",
-"FEDDDCCCCBBAB",
-"FEDDDCCCCBABC",
-"FDDDDCCCCABBC",
-"EDDCCCCBACCCC",
-"EDCCCCBABCCCC",
-"EDCCCBABCCCCC",
-"EDCCBABCCCCCD",
-"EDCCABCCCDDDD",
-"ECCACCCCCDDDD",
-"ECACCCCCDDDDD",
-"DACCDDDDDDEEE",
-"ADEEEEEEEFFFF"
-</pre>
+++ /dev/null
-<title>xtc file format</title>
-<H3>Description</H3>
-The xtc format is a <b>portable</b> format for trajectories.
-It uses the <i>xdr</i> routines for writing and reading
-data which was created for the Unix NFS system. The trajectories
-are written using a reduced precision algorithm which works
-in the following way: the coordinates (in nm) are multiplied by a scale
-factor, typically 1000, so that you have coordinates in pm.
-These are rounded to integer values. Then several other tricks are
-performed, for instance making use of the fact that atoms close
-in sequence are usually close in space too (e.g. a water molecule).
-To this end, the <i>xdr</i> library is extended with a special routine
-to write 3-D float coordinates. <!-- link is broken--><!-- This routine was written by Frans van Hoesel
-as part of an Europort project, and can be obtained through <a href="http://hpcv100.rc.rug.nl/xdrf.html">this link</a>.-->
-<p>
-All the data is stored using calls to <i>xdr</i> routines.
-
-<dl>
-<dt><b>int</b> magic
- <dd>A magic number, for the current file version its value is 1995.
-<dt><b>int</b> natoms
- <dd>The number of atoms in the trajectory.
-<dt><b>int</b> step
- <dd>The simulation step.
-<dt><b>float</b> time
- <dd>The simulation time.
-<dt><b>float</b> box[3][3]
- <dd>The computational box which is stored as a set of three basis
- vectors, to allow for triclinic PBC. For a rectangular box the
- box edges are stored on the diagonal of the matrix.
-<dt><b>3dfcoord</b> x[natoms]
- <dd>The coordinates themselves stored in reduced precision.
- Please note that when the number of atoms is smaller than 9
- no reduced precision is used.
-</dl>
-
-<h3>Using xtc in your "C" programs</h3>
-To read and write these files the following "C" routines are available:
-<pre>
-/* All functions return 1 if successful, 0 otherwise */
-
-extern int open_xtc(XDR *xd,char *filename,char *mode);
-/* Open a file for xdr I/O */
-
-extern void close_xtc(XDR *xd);
-/* Close the file for xdr I/O */
-
-extern int read_first_xtc(XDR *xd,char *filename,
- int *natoms,int *step,real *time,
- matrix box,rvec **x,real *prec);
-/* Open xtc file, read xtc file first time, allocate memory for x */
-
-extern int read_next_xtc(XDR *xd,
- int *natoms,int *step,real *time,
- matrix box,rvec *x,real *prec);
-/* Read subsequent frames */
-
-extern int write_xtc(XDR *xd,
- int natoms,int step,real time,
- matrix box,rvec *x,real prec);
-/* Write a frame to xtc file */
-</pre>
-To use the library function include <tt>"gromacs/fileio/xtcio.h"</tt>
-in your file and link with <tt>-lgmx.$(CPU)</tt>
-<p>
-
-<h3>Using xtc in your FORTRAN programs</h3>
-To read and write these in a FORTRAN program use the calls to
-<tt>readxtc</tt> and <tt>writextc</tt> as in the following sample program
-which reads and xtc file and copies it to a new one:
-<pre>
- program testxtc
-
- parameter (maxatom=10000,maxx=3*maxatom)
- integer xd,xd2,natoms,step,ret,i
- real time,box(9),x(maxx)
-
- call xdrfopen(xd,"test.xtc","r",ret)
- print *,'opened test.xtc, ret=',ret
- call xdrfopen(xd2,"testout.xtc","w",ret)
- print *,'opened testout.xtc, ret=',ret
-
- 10 call readxtc(xd,natoms,step,time,box,x,prec,ret)
-
- if ( ret .eq. 1 ) then
- call writextc(xd2,natoms,step,time,box,x,prec,ret)
- else
- print *,'Error reading xtc'
- endif
-
- stop
- end
-</pre>
-To link your program use <tt>-L$(GMXHOME)/lib/$(CPU) -lxtcf</tt>
-on your linker command line.
-The source for this test can be found in file
-<tt>$(GMXHOME)/src/gmxlib/testxtcf.f</ff>.
+++ /dev/null
-<title>xvgr file format</title>
-<H3>Description</H3>
-Almost all output from GROMACS analysis tools is ready as input for
-Grace, formerly known as Xmgr. We use Grace, because it is very flexible, and it is also
-free software. It produces PostScript(tm) output, which is very suitable
-for inclusion in eg. LaTeX documents, but also for other word processors.
-<p>
-A sample Grace session with GROMACS data is shown below.<br><br>
-<img src="../images/xvgr.gif" alt="xvgr window"> <br>
================
* `Flow Chart <online/flow.html>`_
-* `File Formats <online/files.html>`_
File formats
============
-TODO in future patch: gather information from
-``docs/old-html/online/*html``, convert to .rst, update for accuracy,
-organize here.
+.. TODO in future patch: update for accuracy, organize better, improve formatting
+
+Summary of file formats
+^^^^^^^^^^^^^^^^^^^^^^^
+
+Parameter files
+---------------
+
+:ref:`mdp`
+ run parameters, input for :ref:`gmx grompp` and :ref:`gmx convert-tpr`
+
+:ref:`m2p`
+ input for :ref:`gmx xpm2ps`
+
+Structure files
+---------------
+
+:ref:`gro`
+ GROMACS format
+:ref:`g96`
+ GROMOS-96 format
+:ref:`pdb`
+ brookhaven Protein DataBank format
+**Structure+mass(db):** :ref:`tpr`, :ref:`gro`, :ref:`g96`, or :ref:`pdb`
+ Structure and mass input for analysis tools.
+ When gro or pdb is used approximate masses will be read from the mass database.
+
+Topology files
+--------------
+
+:ref:`top`
+ system topology (ascii)
+:ref:`itp`
+ include topology (ascii)
+:ref:`rtp`
+ residue topology (ascii)
+:ref:`ndx`
+ index file
+
+Run Input files
+---------------
+
+:ref:`tpr`
+ system topology, parameters, coordinates and velocities (binary, portable)
+
+Trajectory files
+----------------
+
+:ref:`tng`
+ Any kind of data (compressed, portable, any precision)
+:ref:`trr`
+ x, v and f (binary, full precision, portable)
+:ref:`xtc`
+ x only (compressed, portable, any precision)
+:ref:`gro`
+ x and v (ascii, any precision)
+:ref:`g96`
+ x only (ascii, fixed high precision)
+:ref:`pdb`
+ x only (ascii, reduced precision)
+**Formats for full-precision data:**
+ :ref:`tng` or :ref:`trr`
+**Generic trajectory formats:**
+ :ref:`tng`, :ref:`xtc`, :ref:`trr`, :ref:`gro`, :ref:`g96`, or :ref:`pdb`
+
+Energy files
+------------
+
+:ref:`ene`
+ energies, temperature, pressure, box size, density and virials (binary)
+:ref:`edr`
+ energies, temperature, pressure, box size, density and virials (binary, portable)
+**Generic energy formats:**
+ :ref:`edr` or :ref:`ene`
+
+Other files
+-----------
+
+:ref:`dat`
+ generic, preferred for input
+:ref:`edi`
+ essential dynamics constraints input for :ref:`gmx mdrun`
+:ref:`edo`
+ essential dynamics constraints output for :ref:`gmx mdrun`
+:ref:`eps`
+ Encapsulated Postscript
+:ref:`log`
+ log file
+:ref:`map`
+ colormap input for :ref:`gmx do_dssp`
+:ref:`mtx`
+ binary matrix data
+:ref:`out`
+ generic, preferred for output
+:ref:`tex`
+ LaTeX input
+:ref:`xpm`
+ ascii matrix data, use :ref:`gmx xpm2ps` to convert to :ref:`eps`
+:ref:`xvg`
+ xvgr input
+
+File format details
+^^^^^^^^^^^^^^^^^^^
+
+.. _cpt:
+
+cpt
+---
+
+The cpt file extension stands for portable checkpoint file.
+The complete state of the simulation is stored in the checkpoint file,
+including extended thermostat/barostat variables, random number states
+and NMR time averaged data.
+With domain decomposition also the some decomposition setup information
+is stored.
+
+See also :ref:`gmx mdrun`.
+
+.. _dat:
+
+dat
+---
+
+Files with the dat file extension contain generic input or output.
+As it is not possible
+to categorise all data file formats, GROMACS has a generic file format called
+dat of which no format is given.
+
+.. _dlg:
+
+dlg
+---
+
+The dlg file format is used as input for the :ref:`gmx view`
+trajectory viewer. These files are not meant to be altered by the end user.
+
+Sample
+++++++
+
+::
+
+ grid 39 18 {
+
+ group "Bond Options" 1 1 16 9 {
+ radiobuttons { " Thin Bonds" " Fat Bonds" " Very Fat Bonds" " Spheres" }
+ "bonds" "Ok" " F" "help bonds"
+ }
+
+ group "Other Options" 18 1 20 13 {
+ checkbox " Show Hydrogens" "" "" "FALSE" "help opts"
+ checkbox " Draw plus for atoms" "" "" "TRUE" "help opts"
+ checkbox " Show Box" "" "" "TRUE" "help opts"
+ checkbox " Remove PBC" "" "" "FALSE" "help opts"
+ checkbox " Depth Cueing" "" "" "TRUE" "help opts"
+ edittext "Skip frames: " "" "" "0" "help opts"
+ }
+
+ simple 1 15 37 2 {
+ defbutton "Ok" "Ok" "Ok" "Ok" "help bonds"
+ }
+
+ }
+
+.. _edi:
+
+edi
+---
+
+Files with the edi file extension contain information for :ref:`gmx mdrun`
+to run Molecular Dynamics with Essential Dynamics constraints.
+
+.. WEDSAM and ESSDYN seem to have vanished from WhatIf and the web
+ These files can be generated by the program <tt>WEDSAM</tt> which uses
+ output from the programs in the <tt>ESSDYN</tt> menu of the
+ <A HREF="http://www.sander.embl-heidelberg.de/whatif/">WHAT IF</A> program.
+
+.. _edo:
+
+edo
+---
+
+Files with the edo file extension are generated by :ref:`gmx mdrun`
+if Molecular Dynamics is performed with Essential Dynamics
+constraints. Depending on the parameters set in the :ref:`edi`:
+file, edo files may contain projections of positions,
+velocities and forces onto selected eigenvectors during the run as well
+as RMSD values, or information about specific types of constraints.
+Specific results can be extracted from the edo files with standard Unix
+utilities like ``awk``.
+
+.. _edr:
+
+edr
+---
+
+The edr file extension stands for portable energy file.
+The energies are stored using the xdr protocol.
+
+See also :ref:`gmx energy`.
+
+.. _ene:
+
+ene
+---
+
+The ene file extension stands for binary energy file. It holds the
+energies as generated during your :ref:`gmx mdrun`.
+
+The file can be transformed to a portable energy file (portable
+accross hardware platforms), the :ref:`edr` file using the program
+:ref:`gmx eneconv`.
+
+See also :ref:`gmx energy`.
+
+.. _eps:
+
+eps
+---
+
+The eps file format is not a special GROMACS format, but just a
+variant of the standard PostScript(tm). A sample eps file as
+generated by the :ref:`gmx xpm2ps` program is
+included below. It shows the secondary structure of a peptide as a function
+of time.
+
+.. image:: plotje.gif
+ :alt: hallo
+
+.. _g96:
+
+g96
+---
+
+A file with the g96 extension can be a GROMOS-96 initial/final
+configuration file or a coordinate trajectory file or a combination of both.
+The file is fixed format, all floats are written as 15.9 (files can get huge).
+GROMACS supports the following data blocks in the given order:
+
+ * Header block:
+
+ - ``TITLE`` (mandatory)
+
+ * Frame blocks:
+
+ - ``TIMESTEP`` (optional)
+ - ``POSITION/POSITIONRED`` (mandatory)
+ - ``VELOCITY/VELOCITYRED`` (optional)
+ - ``BOX`` (optional)
+
+See the GROMOS-96 manual for a complete description of the blocks.
+
+Note that all GROMACS programs can read compressed or g-zipped files.
+
+.. _gro:
+
+gro
+---
+
+Files with the gro file extension contain a molecular structure in
+Gromos87 format. gro files can be used as trajectory by simply
+concatenating files. An attempt will be made to read a time value from
+the title string in each frame, which should be preceded by
+'``t=``', as in the sample below.
+
+A sample piece is included below::
+
+ MD of 2 waters, t= 0.0
+ 6
+ 1WATER OW1 1 0.126 1.624 1.679 0.1227 -0.0580 0.0434
+ 1WATER HW2 2 0.190 1.661 1.747 0.8085 0.3191 -0.7791
+ 1WATER HW3 3 0.177 1.568 1.613 -0.9045 -2.6469 1.3180
+ 2WATER OW1 4 1.275 0.053 0.622 0.2519 0.3140 -0.1734
+ 2WATER HW2 5 1.337 0.002 0.680 -1.0641 -1.1349 0.0257
+ 2WATER HW3 6 1.326 0.120 0.568 1.9427 -0.8216 -0.0244
+ 1.82060 1.82060 1.82060
+
+Lines contain the following information (top to bottom):
+
+ * title string (free format string, optional time in ps after '``t=``')
+ * number of atoms (free format integer)
+ * one line for each atom (fixed format, see below)
+ * box vectors (free format, space separated reals), values:
+ v1(x) v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y),
+ the last 6 values may be omitted (they will be set to zero).
+ Gromacs only supports boxes with v1(y)=v1(z)=v2(z)=0.
+
+This format is fixed, ie. all columns are in a fixed
+position. Optionally (for now only yet with trjconv) you can write gro
+files with any number of decimal places, the format will then be
+``n+5`` positions with ``n`` decimal places (``n+1``
+for velocities) in stead of ``8`` with ``3`` (with
+``4`` for velocities). Upon reading, the precision will be
+inferred from the distance between the decimal points (which will be
+``n+5``). Columns contain the following information (from left to
+right):
+
+ * residue number (5 positions, integer)
+ * residue name (5 characters)
+ * atom name (5 characters)
+ * atom number (5 positions, integer)
+ * position (in nm, x y z in 3 columns, each 8 positions with 3 decimal places)
+ * velocity (in nm/ps (or km/s), x y z in 3 columns, each 8 positions with 4 decimal places)
+
+Note that separate molecules or ions (e.g. water or Cl-) are regarded
+as residues. If you want to write such a file in your own program
+without using the GROMACS libraries you can use the following formats:
+
+C format
+ ``"%5d%-5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f"``
+Fortran format
+ ``(i5,2a5,i5,3f8.3,3f8.4)``
+Pascal format
+ This is left as an exercise for the user
+
+Note that this is the format for writing, as in the above example
+fields may be written without spaces, and therefore can not be read
+with the same format statement in C.
+
+.. _hdb:
+
+hdb
+---
+
+The hdb file extension stands for hydrogen database
+Such a file is needed by :ref:`gmx pdb2gmx`
+when building hydrogen atoms that were either originally missing, or that
+were removed with ``-ignh``.
+
+.. _itp:
+
+itp
+---
+
+The itp file extension stands for include toplogy. These files are included in
+topology files (with the :ref:`top` extension).
+
+.. _log:
+
+log
+---
+
+Logfiles are generated by some GROMACS programs and are usually in
+human-readable format. Use ``more logfile``.
+
+.. _m2p:
+
+m2p
+---
+
+The m2p file format contains input options for the
+:ref:`gmx xpm2ps` program. All of these options
+are very easy to comprehend when you look at the PosScript(tm) output
+from :ref:`gmx xpm2ps`.
+
+::
+
+ ; Command line options of xpm2ps override the parameters in this file
+ black&white = no ; Obsolete
+ titlefont = Times-Roman ; A PostScript Font
+ titlefontsize = 20 ; Font size (pt)
+ legend = yes ; Show the legend
+ legendfont = Times-Roman ; A PostScript Font
+ legendlabel = ; Used when there is none in the .xpm
+ legend2label = ; Used when merging two xpm's
+ legendfontsize = 14 ; Font size (pt)
+ xbox = 2.0 ; x-size of a matrix element
+ ybox = 2.0 ; y-size of a matrix element
+ matrixspacing = 20.0 ; Space between 2 matrices
+ xoffset = 0.0 ; Between matrix and bounding box
+ yoffset = 0.0 ; Between matrix and bounding box
+ x-major = 20 ; Major ticks on x axis every .. frames
+ x-minor = 5 ; Id. Minor ticks
+ x-firstmajor = 0 ; First frame for major tick
+ x-majorat0 = no ; Major tick at first frame
+ x-majorticklen = 8.0 ; x-majorticklength
+ x-minorticklen = 4.0 ; x-minorticklength
+ x-label = ; Used when there is none in the .xpm
+ x-fontsize = 16 ; Font size (pt)
+ x-font = Times-Roman ; A PostScript Font
+ x-tickfontsize = 10 ; Font size (pt)
+ x-tickfont = Helvetica ; A PostScript Font
+ y-major = 20
+ y-minor = 5
+ y-firstmajor = 0
+ y-majorat0 = no
+ y-majorticklen = 8.0
+ y-minorticklen = 4.0
+ y-label =
+ y-fontsize = 16
+ y-font = Times-Roman
+ y-tickfontsize = 10
+ y-tickfont = Helvetica
+
+.. _map:
+
+map
+---
+
+This file maps matrix data to RGB values which is used by the
+:ref:`gmx do_dssp` program.
+
+The format of this file is as follow: first line number of elements
+in the colormap. Then for each line: The first character is
+a code for the secondary structure type.
+Then comes a string for use in the legend of the plot and then the
+R (red) G (green) and B (blue) values.
+
+In this case the colors are
+(in order of appearance): white, red, black, cyan, yellow, blue, magenta, orange.
+
+::
+
+ 8
+ ~ Coil 1.0 1.0 1.0
+ E B-Sheet 1.0 0.0 0.0
+ B B-Bridge 0.0 0.0 0.0
+ S Bend 0.0 0.8 0.8
+ T Turn 1.0 1.0 0.0
+ H A-Helix 0.0 0.0 1.0
+ G 3-Helix 1.0 0.0 1.0
+ I 5-Helix 1.0 0.6 0.0
+
+.. _mdp:
+
+mdp
+---
+
+See the user guide for a detailed description of the options.
+
+Below is a sample mdp file.
+The ordering of the items is not important, but if you enter the same
+thing twice, the **last** is used (:ref:`gmx grompp` gives you a note when
+overriding values). Dashes and underscores on the left hand side are ignored.
+
+The values of the options are reasonable values for a 1 nanosecond
+MD run of a protein in a box of water.
+
+::
+
+ title = Yo
+ cpp = /lib/cpp
+ include = -I../top
+ define =
+ integrator = md
+ dt = 0.002
+ nsteps = 500000
+ nstxout = 5000
+ nstvout = 5000
+ nstlog = 5000
+ nstenergy = 250
+ nstxout-compressed = 250
+ compressed-x-grps = Protein
+ energygrps = Protein SOL
+ nstlist = 10
+ ns-type = grid
+ rlist = 0.8
+ coulombtype = cut-off
+ rcoulomb = 1.4
+ rvdw = 0.8
+ tcoupl = Berendsen
+ tc-grps = Protein SOL
+ tau-t = 0.1 0.1
+ ref-t = 300 300
+ Pcoupl = Berendsen
+ tau-p = 1.0
+ compressibility = 4.5e-5
+ ref-p = 1.0
+ gen-vel = yes
+ gen-temp = 300
+ gen-seed = 173529
+ constraints = all-bonds
+
+With this input :ref:`gmx grompp` will produce
+an ``mdout.mdp`` with all the options and descriptions:
+
+::
+
+ ; VARIOUS PREPROCESSING OPTIONS =
+ title = Yo
+ cpp = /lib/cpp
+ include = -I../top
+ define =
+
+ ; RUN CONTROL PARAMETERS =
+ integrator = md
+ ; start time and timestep in ps =
+ tinit = 0
+ dt = 0.002
+ nsteps = 500000
+ ; number of steps for center of mass motion removal =
+ nstcomm = 1
+ comm-grps =
+
+ ; LANGEVIN DYNAMICS OPTIONS =
+ ; Temperature, friction coefficient (amu/ps) and random seed =
+ bd-temp = 300
+ bd-fric = 0
+ ld-seed = 1993
+
+ ; ENERGY MINIMIZATION OPTIONS =
+ ; Force tolerance and initial step-size =
+ emtol = 100
+ emstep = 0.01
+ ; Max number of iterations in relax-shells =
+ niter = 20
+ ; Frequency of steepest descents steps when doing CG =
+ nstcgsteep = 1000
+
+ ; OUTPUT CONTROL OPTIONS =
+ ; Output frequency for coords (x), velocities (v) and forces (f) =
+ nstxout = 5000
+ nstvout = 5000
+ nstfout = 0
+ ; Output frequency for energies to log file and energy file =
+ nstlog = 5000
+ nstenergy = 250
+ ; Output frequency and precision for xtc file =
+ nstxout-compressed = 250
+ compressed-x-precision = 1000
+ ; This selects the subset of atoms for the xtc file. You can =
+ ; select multiple groups. By default all atoms will be written. =
+ compressed-x-grps = Protein
+ ; Selection of energy groups =
+ energygrps = Protein SOL
+
+ ; NEIGHBORSEARCHING PARAMETERS =
+ ; nblist update frequency =
+ nstlist = 10
+ ; ns algorithm (simple or grid) =
+ ns-type = grid
+ ; Periodic boundary conditions: xyz or none =
+ pbc = xyz
+ ; nblist cut-off =
+ rlist = 0.8
+
+ ; OPTIONS FOR ELECTROSTATICS AND VDW =
+ ; Method for doing electrostatics =
+ coulombtype = cut-off
+ rcoulomb-switch = 0
+ rcoulomb = 1.4
+ ; Dielectric constant (DC) for cut-off or DC of reaction field =
+ epsilon-r = 1
+ ; Method for doing Van der Waals =
+ vdw-type = Cut-off
+ ; cut-off lengths =
+ rvdw-switch = 0
+ rvdw = 0.8
+ ; Apply long range dispersion corrections for Energy and Pressure =
+ DispCorr = No
+ ; Spacing for the PME/PPPM FFT grid =
+ fourierspacing = 0.12
+ ; FFT grid size, when a value is 0 fourierspacing will be used =
+ fourier-nx = 0
+ fourier-ny = 0
+ fourier-nz = 0
+ ; EWALD/PME/PPPM parameters =
+ pme-order = 4
+ ewald-rtol = 1e-05
+ epsilon-surface = 0
+
+ ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
+ ; Temperature coupling =
+ tcoupl = Berendsen
+ ; Groups to couple separately =
+ tc-grps = Protein SOL
+ ; Time constant (ps) and reference temperature (K) =
+ tau-t = 0.1 0.1
+ ref-t = 300 300
+ ; Pressure coupling =
+ Pcoupl = Berendsen
+ Pcoupltype = Isotropic
+ ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
+ tau-p = 1.0
+ compressibility = 4.5e-5
+ ref-p = 1.0
+
+ ; SIMULATED ANNEALING CONTROL =
+ annealing = no
+ ; Time at which temperature should be zero (ps) =
+ zero-temp-time = 0
+
+ ; GENERATE VELOCITIES FOR STARTUP RUN =
+ gen-vel = yes
+ gen-temp = 300
+ gen-seed = 173529
+
+ ; OPTIONS FOR BONDS =
+ constraints = all-bonds
+ ; Type of constraint algorithm =
+ constraint-algorithm = Lincs
+ ; Do not constrain the start configuration =
+ unconstrained-start = no
+ ; Relative tolerance of shake =
+ shake-tol = 0.0001
+ ; Highest order in the expansion of the constraint coupling matrix =
+ lincs-order = 4
+ ; Lincs will write a warning to the stderr if in one step a bond =
+ ; rotates over more degrees than =
+ lincs-warnangle = 30
+ ; Convert harmonic bonds to morse potentials =
+ morse = no
+
+ ; NMR refinement stuff =
+ ; Distance restraints type: No, Simple or Ensemble =
+ disre = No
+ ; Force weighting of pairs in one distance restraint: Equal or Conservative =
+ disre-weighting = Equal
+ ; Use sqrt of the time averaged times the instantaneous violation =
+ disre-mixed = no
+ disre-fc = 1000
+ disre-tau = 0
+ ; Output frequency for pair distances to energy file =
+ nstdisreout = 100
+
+ ; Free energy control stuff =
+ free-energy = no
+ init-lambda = 0
+ delta-lambda = 0
+ sc-alpha = 0
+ sc-sigma = 0.3
+
+ ; Non-equilibrium MD stuff =
+ acc-grps =
+ accelerate =
+ freezegrps =
+ freezedim =
+ cos-acceleration = 0
+ energygrp-excl =
+
+ ; Electric fields =
+ ; Format is number of terms (int) and for all terms an amplitude (real) =
+ ; and a phase angle (real) =
+ E-x =
+ E-xt =
+ E-y =
+ E-yt =
+ E-z =
+ E-zt =
+
+ ; User defined thingies =
+ user1-grps =
+ user2-grps =
+ userint1 = 0
+ userint2 = 0
+ userint3 = 0
+ userint4 = 0
+ userreal1 = 0
+ userreal2 = 0
+ userreal3 = 0
+ userreal4 = 0
+
+.. _mtx:
+
+mtx
+---
+
+Files with the mtx file extension contain a matrix.
+The file format is identical to the :ref:`trr` format.
+Currently this file format is only used for hessian matrices,
+which are produced with :ref:`gmx mdrun` and read by
+:ref:`gmx nmeig`.
+
+.. _ndx:
+
+ndx
+---
+
+The GROMACS index file (usually called index.ndx) contains some
+user definable sets of atoms. The file can be read by
+most analysis programs, by the graphics program
+(:ref:`gmx view`)
+and by the preprocessor (:ref:`gmx grompp`).
+Most of these programs create default index groups when no index
+file is supplied, so you only need to make an index file when you need special
+groups.
+
+First the group name is written between square brackets.
+The following atom numbers may be spread out over as many lines as you like.
+The atom numbering starts at 1.
+
+An example file is here:
+
+::
+
+ [ Oxygen ]
+ 1 4 7
+ [ Hydrogen ]
+ 2 3 5 6
+ 8 9
+
+There are two groups, and total nine atoms. The first group
+**Oxygen** has 3 elements.
+The second group **Hydrogen** has 6 elements.
+
+An index file generation tool is available:
+:ref:`gmx make_ndx`.
+
+.. _out:
+
+out
+---
+
+Files with the out file extension contain generic output. As it is not possible
+to categorise all data file formats, GROMACS has a generic file format called
+out of which no format is given.
+
+.. _pdb:
+
+pdb
+---
+
+
+Files with the :ref:`pdb` extension are molecular
+structure files in the protein databank file format. The protein
+databank file format describes the positions of atoms in a molecular
+structure. Coordinates are read from the ATOM and HETATM records,
+until the file ends or an ENDMDL record is encountered.
+GROMACS programs can read and write a simlation box in the
+CRYST1 entry.
+The pdb format can also be used as a trajectory format:
+several structures, seperated by ENDMDL, can be read from
+or written to one file.
+
+Example
++++++++
+
+An pdb file should look like this::
+
+ ATOM 1 H1 LYS 1 14.260 6.590 34.480 1.00 0.00
+ ATOM 2 H2 LYS 1 13.760 5.000 34.340 1.00 0.00
+ ATOM 3 N LYS 1 14.090 5.850 33.800 1.00 0.00
+ ATOM 4 H3 LYS 1 14.920 5.560 33.270 1.00 0.00
+ ...
+ ...
+
+.. _rtp:
+
+rtp
+---
+
+The rtp file extension stands for residue toplogy.
+Such a file is needed by :ref:`gmx pdb2gmx`
+to make a GROMACS topology for a protein contained in a :ref:`pdb`
+file. The file contains the default interaction type for the 4 bonded
+interactions and residue entries, which consist of atoms and
+optionally bonds, angles dihedrals and impropers.
+Parameters can be added to bonds, angles, dihedrals and impropers,
+these parameters override the standard parameters in the :ref:`itp` files.
+This should only be used in special cases.
+Instead of parameters a string can be added for each bonded interaction,
+the string is copied to the :ref:`top` file,
+this is used for the GROMOS96 forcefield.
+
+:ref:`gmx pdb2gmx` automatically generates all angles,
+this means that the ``[angles]`` field is only
+useful for overriding :ref:`itp` parameters.
+
+:ref:`gmx pdb2gmx` automatically generates one proper
+dihedral for every rotatable bond, preferably on heavy atoms.
+When the ``[dihedrals]`` field is used, no other dihedrals will
+be generated for the bonds corresponding to the specified dihedrals.
+It is possible to put more than one dihedral on a rotatable bond.
+
+:ref:`gmx pdb2gmx` sets the number exclusions to 3, which
+means that interactions between atoms connected by at most 3 bonds are
+excluded. Pair interactions are generated for all pairs of atoms which are
+seperated by 3 bonds (except pairs of hydrogens).
+When more interactions need to be excluded, or some pair interactions should
+not be generated, an ``[exclusions]`` field can be added, followed by
+pairs of atom names on seperate lines. All non-bonded and pair interactions
+between these atoms will be excluded.
+
+A sample is included below.
+
+::
+
+ [ bondedtypes ] ; mandatory
+ ; bonds angles dihedrals impropers
+ 1 1 1 2 ; mandatory
+
+ [ GLY ] ; mandatory
+
+ [ atoms ] ; mandatory
+ ; name type charge chargegroup
+ N N -0.280 0
+ H H 0.280 0
+ CA CH2 0.000 1
+ C C 0.380 2
+ O O -0.380 2
+
+ [ bonds ] ; optional
+ ;atom1 atom2 b0 kb
+ N H
+ N CA
+ CA C
+ C O
+ -C N
+
+ [ exclusions ] ; optional
+ ;atom1 atom2
+
+ [ angles ] ; optional
+ ;atom1 atom2 atom3 th0 cth
+
+ [ dihedrals ] ; optional
+ ;atom1 atom2 atom3 atom4 phi0 cp mult
+
+ [ impropers ] ; optional
+ ;atom1 atom2 atom3 atom4 q0 cq
+ N -C CA H
+ -C -CA N -O
+
+
+ [ ZN ]
+ [ atoms ]
+ ZN ZN 2.000 0
+
+.. _tex:
+
+tex
+---
+
+We use **LaTeX** for *document* processing.
+Although the input is not so
+user friendly, it has some advantages over *word* processors.
+
+ * **LaTeX** knows a lot about formatting, probably much more than you.
+ * The input is clear, you always know what you are doing
+ * It makes anything from letters to a thesis
+ * Much more...
+
+.. _tng:
+
+tng
+---
+
+Files with the ``.tng`` file extension can contain all kinds of data
+related to the trajectory of a simulation. For example, it might
+contain coordinates, velocities, forces and/or energies. Various :ref:`mdp`
+file options control which of these are written by mdrun, whether data
+is written with compression, and how lossy that compression can be.
+This file is in portable binary format an can be read with :ref:`gmx dump`.
+
+.. parsed-literal:
+
+ % :ref:`gmx dump` -f traj.tng
+
+or if you're not such a fast reader::
+
+ % gmx dump -f traj.tng | less
+
+You can also get a quick look in the contents of the file (number of
+frames etc.) using:
+
+.. parsed-literal:
+
+ % :ref:`gmx check` -f traj.tng
+
+.. _top:
+
+top
+---
+
+The top file extension stands for topology. It is an ascii file which is
+read by :ref:`gmx grompp` which processes it
+and creates a binary topology (:ref:`tpr` file).
+
+A sample file is included below::
+
+ ;
+ ; Example topology file
+ ;
+ [ defaults ]
+ ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
+ 1 1 no 1.0 1.0
+
+ ; The force field files to be included
+ #include "rt41c5.itp"
+
+ [ moleculetype ]
+ ; name nrexcl
+ Urea 3
+
+ [ atoms ]
+ ; nr type resnr residu atom cgnr charge
+ 1 C 1 UREA C1 1 0.683
+ 2 O 1 UREA O2 1 -0.683
+ 3 NT 1 UREA N3 2 -0.622
+ 4 H 1 UREA H4 2 0.346
+ 5 H 1 UREA H5 2 0.276
+ 6 NT 1 UREA N6 3 -0.622
+ 7 H 1 UREA H7 3 0.346
+ 8 H 1 UREA H8 3 0.276
+
+ [ bonds ]
+ ; ai aj funct c0 c1
+ 3 4 1 1.000000e-01 3.744680e+05
+ 3 5 1 1.000000e-01 3.744680e+05
+ 6 7 1 1.000000e-01 3.744680e+05
+ 6 8 1 1.000000e-01 3.744680e+05
+ 1 2 1 1.230000e-01 5.020800e+05
+ 1 3 1 1.330000e-01 3.765600e+05
+ 1 6 1 1.330000e-01 3.765600e+05
+
+ [ pairs ]
+ ; ai aj funct c0 c1
+ 2 4 1 0.000000e+00 0.000000e+00
+ 2 5 1 0.000000e+00 0.000000e+00
+ 2 7 1 0.000000e+00 0.000000e+00
+ 2 8 1 0.000000e+00 0.000000e+00
+ 3 7 1 0.000000e+00 0.000000e+00
+ 3 8 1 0.000000e+00 0.000000e+00
+ 4 6 1 0.000000e+00 0.000000e+00
+ 5 6 1 0.000000e+00 0.000000e+00
+
+ [ angles ]
+ ; ai aj ak funct c0 c1
+ 1 3 4 1 1.200000e+02 2.928800e+02
+ 1 3 5 1 1.200000e+02 2.928800e+02
+ 4 3 5 1 1.200000e+02 3.347200e+02
+ 1 6 7 1 1.200000e+02 2.928800e+02
+ 1 6 8 1 1.200000e+02 2.928800e+02
+ 7 6 8 1 1.200000e+02 3.347200e+02
+ 2 1 3 1 1.215000e+02 5.020800e+02
+ 2 1 6 1 1.215000e+02 5.020800e+02
+ 3 1 6 1 1.170000e+02 5.020800e+02
+
+ [ dihedrals ]
+ ; ai aj ak al funct c0 c1 c2
+ 2 1 3 4 1 1.800000e+02 3.347200e+01 2.000000e+00
+ 6 1 3 4 1 1.800000e+02 3.347200e+01 2.000000e+00
+ 2 1 3 5 1 1.800000e+02 3.347200e+01 2.000000e+00
+ 6 1 3 5 1 1.800000e+02 3.347200e+01 2.000000e+00
+ 2 1 6 7 1 1.800000e+02 3.347200e+01 2.000000e+00
+ 3 1 6 7 1 1.800000e+02 3.347200e+01 2.000000e+00
+ 2 1 6 8 1 1.800000e+02 3.347200e+01 2.000000e+00
+ 3 1 6 8 1 1.800000e+02 3.347200e+01 2.000000e+00
+
+ [ dihedrals ]
+ ; ai aj ak al funct c0 c1
+ 3 4 5 1 2 0.000000e+00 1.673600e+02
+ 6 7 8 1 2 0.000000e+00 1.673600e+02
+ 1 3 6 2 2 0.000000e+00 1.673600e+02
+
+ ; Include SPC water topology
+ #include "spc.itp"
+
+ [ system ]
+ Urea in Water
+
+ [ molecules ]
+ Urea 1
+ SOL 1000
+
+.. _tpr:
+
+tpr
+---
+
+The tpr file extension stands for portable binary run input file. This file
+contains the starting structure of your simulation, the molecular topology
+and all the simulation parameters. Because this file is in binary format it
+cannot be read with a normal editor. To read a portable binary run input
+file type:
+
+.. parsed-literal:
+
+ % :ref:`gmx dump` -s topol.tpr
+
+or if you're not such a fast reader::
+
+ % gmx dump -s topol.tpr | less
+
+You can also compare two tpr files using:
+
+.. parsed-literal:
+
+ % :ref:`gmx check` -s1 top1 -s2 top2 | less
+
+.. _trr:
+
+trr
+---
+
+Files with the trr file extension contain the trajectory of a simulation.
+In this file all the coordinates, velocities, forces and energies are
+printed as you told GROMACS in your mdp file. This file is in portable binary
+format an can be read with :ref:`gmx dump`::
+
+ % gmx dump -f traj.trr
+
+or if you're not such a fast reader::
+
+ % gmx dump -f traj.trr | less
+
+You can also get a quick look in the contents of the file (number of
+frames etc.) using:
+
+.. parsed-literal:
+
+ % :ref:`gmx check` -f traj.trr
+
+.. _xpm:
+
+xpm
+---
+
+The GROMACS xpm file format is compatible with the XPixMap format
+and is used for storing matrix data.
+Thus GROMACS xpm files can be viewed directly with programs like XV.
+Alternatively, they can be imported into GIMP and scaled to 300 DPI,
+using strong antialiasing for font and graphics.
+The first matrix data line in an xpm file corresponds to the last matrix
+row.
+In addition to the XPixMap format, GROMACS xpm files may contain
+extra fields. The information in these fields is used when converting
+an xpm file to EPS with :ref:`gmx xpm2ps`.
+The optional extra field are:
+
+ * Before the ``gv_xpm`` declaration: ``title``, ``legend``,
+ ``x-label``, ``y-label`` and ``type``, all followed by a string.
+ The ``legend`` field determines the legend title.
+ The ``type`` field must be followed by ``"continuous"`` or
+ ``"discrete"``, this determines which type of legend will be drawn in an EPS
+ file, the default type is continuous.
+ * The xpm colormap entries may be followed by a string, which is a label for
+ that color.
+ * Between the colormap and the matrix data, the fields ``x-axis`` and/or
+ ``y-axis`` may be present followed by the tick-marks for that axis.
+
+The example GROMACS xpm file below contains all the extra fields.
+The C-comment delimiters and the colon in the extra fields are optional.
+
+::
+
+ /* XPM */
+ /* This matrix is generated by g_rms. */
+ /* title: "Backbone RMSD matrix" */
+ /* legend: "RMSD (nm)" */
+ /* x-label: "Time (ps)" */
+ /* y-label: "Time (ps)" */
+ /* type: "Continuous" */
+ static char * gv_xpm[] = {
+ "13 13 6 1",
+ "A c #FFFFFF " /* "0" */,
+ "B c #CCCCCC " /* "0.0399" */,
+ "C c #999999 " /* "0.0798" */,
+ "D c #666666 " /* "0.12" */,
+ "E c #333333 " /* "0.16" */,
+ "F c #000000 " /* "0.2" */,
+ /* x-axis: 0 40 80 120 160 200 240 280 320 360 400 440 480 */
+ /* y-axis: 0 40 80 120 160 200 240 280 320 360 400 440 480 */
+ "FEDDDDCCCCCBA",
+ "FEDDDCCCCBBAB",
+ "FEDDDCCCCBABC",
+ "FDDDDCCCCABBC",
+ "EDDCCCCBACCCC",
+ "EDCCCCBABCCCC",
+ "EDCCCBABCCCCC",
+ "EDCCBABCCCCCD",
+ "EDCCABCCCDDDD",
+ "ECCACCCCCDDDD",
+ "ECACCCCCDDDDD",
+ "DACCDDDDDDEEE",
+ "ADEEEEEEEFFFF"
+
+.. _xtc:
+
+xtc
+---
+
+The xtc format is a **portable** format for trajectories.
+It uses the *xdr* routines for writing and reading
+data which was created for the Unix NFS system. The trajectories
+are written using a reduced precision algorithm which works
+in the following way: the coordinates (in nm) are multiplied by a scale
+factor, typically 1000, so that you have coordinates in pm.
+These are rounded to integer values. Then several other tricks are
+performed, for instance making use of the fact that atoms close
+in sequence are usually close in space too (e.g. a water molecule).
+To this end, the <i>xdr</i> library is extended with a special routine
+to write 3-D float coordinates.
+
+.. link is broken: This routine was written by Frans van Hoesel
+ as part of an Europort project, and can be obtained through <a
+ href="http://hpcv100.rc.rug.nl/xdrf.html">this link</a>.
+
+All the data is stored using calls to *xdr* routines.
+
+**int** magic
+ A magic number, for the current file version its value is 1995.
+**int** natoms
+ The number of atoms in the trajectory.
+**int** step
+ The simulation step.
+**float** time
+ The simulation time.
+**float** box[3][3]
+ The computational box which is stored as a set of three basis
+ vectors, to allow for triclinic PBC. For a rectangular box the
+ box edges are stored on the diagonal of the matrix.
+**3dfcoord** x[natoms]
+ The coordinates themselves stored in reduced precision.
+ Please note that when the number of atoms is smaller than 9
+ no reduced precision is used.
+
+Using xtc in your "C" programs
+++++++++++++++++++++++++++++++
+
+To read and write these files the following "C" routines are available::
+
+ /* All functions return 1 if successful, 0 otherwise */
+
+ extern int open_xtc(XDR *xd,char *filename,char *mode);
+ /* Open a file for xdr I/O */
+
+ extern void close_xtc(XDR *xd);
+ /* Close the file for xdr I/O */
+
+ extern int read_first_xtc(XDR *xd,char *filename,
+ int *natoms,int *step,real *time,
+ matrix box,rvec **x,real *prec);
+ /* Open xtc file, read xtc file first time, allocate memory for x */
+
+ extern int read_next_xtc(XDR *xd,
+ int *natoms,int *step,real *time,
+ matrix box,rvec *x,real *prec);
+ /* Read subsequent frames */
+
+ extern int write_xtc(XDR *xd,
+ int natoms,int step,real time,
+ matrix box,rvec *x,real prec);
+ /* Write a frame to xtc file */
+
+To use the library function include ``"gromacs/fileio/xtcio.h"``
+in your file and link with ``-lgmx.$(CPU)``.
+
+Using xtc in your FORTRAN programs
+++++++++++++++++++++++++++++++++++
+
+To read and write these in a FORTRAN program use the calls to
+``readxtc`` and ``writextc`` as in the following sample program
+which reads and xtc file and copies it to a new one::
+
+ program testxtc
+
+ parameter (maxatom=10000,maxx=3*maxatom)
+ integer xd,xd2,natoms,step,ret,i
+ real time,box(9),x(maxx)
+
+ call xdrfopen(xd,"test.xtc","r",ret)
+ print *,'opened test.xtc, ret=',ret
+ call xdrfopen(xd2,"testout.xtc","w",ret)
+ print *,'opened testout.xtc, ret=',ret
+
+ call readxtc(xd,natoms,step,time,box,x,prec,ret)
+
+ if ( ret .eq. 1 ) then
+ call writextc(xd2,natoms,step,time,box,x,prec,ret)
+ else
+ print *,'Error reading xtc'
+ endif
+
+ stop
+ end
+
+To link your program use ``-L$(GMXHOME)/lib/$(CPU) -lxtcf``
+on your linker command line.
+
+.. _xvg:
+
+xvg
+---
+
+Almost all output from GROMACS analysis tools is ready as input for
+Grace, formerly known as Xmgr. We use Grace, because it is very flexible, and it is also
+free software. It produces PostScript(tm) output, which is very suitable
+for inclusion in eg. LaTeX documents, but also for other word processors.
+
+A sample Grace session with GROMACS data is shown below:
+
+.. image:: xvgr.gif
+ :alt: hallo
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The molecular topology file is generated by the program :ref:`gmx pdb2gmx`.
-:ref:`gmx pdb2gmx` translates a PDB_ structure file of any
+:ref:`gmx pdb2gmx` translates a :ref:`PDB` structure file of any
peptide or protein to a molecular topology file. This topology file
contains a complete description of all the interactions in your
peptide or protein.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
When :ref:`gmx pdb2gmx` is executed to generate a molecular topology, it
-also translates the structure file (pdb_ file) to a GROMOS structure
-file (gro_ file). The main difference between a pdb_ file and a gromos
-file is their format and that a gro_ file can also hold
+also translates the structure file (:ref:`pdb` file) to a GROMOS structure
+file (:ref:`gro` file). The main difference between a :ref:`pdb` file and a gromos
+file is their format and that a :ref:`gro` file can also hold
velocities. However, if you do not need the velocities, you can also
-use a PDB_ file in all programs. To generate a box of solvent
+use a :ref:`PDB` file in all programs. To generate a box of solvent
molecules around the peptide, the program :ref:`gmx solvate` is
used. First the program :ref:`gmx editconf` should be used to define a box
of appropriate size around the molecule. :ref:`gmx solvate` solvates a
Molecular Dynamics parameter file (``.mdp``)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-The Molecular Dynamics Parameter (mdp_) file contains all information
+The Molecular Dynamics Parameter (:ref:`mdp`) file contains all information
about the Molecular Dynamics simulation itself e.g. time-step, number
of steps, temperature, pressure etc. The easiest way of handling such
-a file is by adapting a sample mdp_ file. A `sample mdp file`_ is
-available.
+a file is by adapting a sample :ref:`mdp` file. A :ref:`sample mdp file <mdp>`
+is available.
Index file (``.ndx``)
^^^^^^^^^^^^^^^^^^^^^
Run input file (``.tpr``)
^^^^^^^^^^^^^^^^^^^^^^^^^
-The next step is to combine the molecular structure (gro_ file),
-topology (top_ file) MD-parameters (mdp_ file) and (optionally) the
-index file (ndx_) to generate a run input file (tpr_ extension). This
+The next step is to combine the molecular structure (:ref:`gro` file),
+topology (:ref:`top` file) MD-parameters (:ref:`mdp` file) and (optionally) the
+index file (:ref:`ndx`) to generate a run input file (:ref:`tpr` extension). This
file contains all information needed to start a simulation with
|Gromacs|. The :ref:`gmx grompp` program processes all input files and
-generates the run input tpr_ file.
+generates the run input :ref:`tpr` file.
Trajectory file (``.trr``, ``.tng``, or ``.xtc``)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
program which starts the simulation is called :ref:`gmx mdrun` (or
sometimes just mdrun, or mdrun_mpi). The only input file of :ref:`gmx mdrun`
that you usually need in order to start a run is the run input
-file (tpr_ file). The typical output files of :ref:`gmx mdrun` are the
-trajectory file (trr_ file), a logfile (log_ file), and perhaps a
-checkpoint file (cpt_ file).
+file (:ref:`tpr` file). The typical output files of :ref:`gmx mdrun` are the
+trajectory file (:ref:`trr` file), a logfile (:ref:`log` file), and perhaps a
+checkpoint file (:ref:`cpt` file).
Tutorial material
-----------------
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff
