From 555e0b3b4f0369ba1bbd3f57f9c8f5354558ee04 Mon Sep 17 00:00:00 2001 From: Teemu Murtola Date: Sat, 7 Feb 2015 07:11:25 +0200 Subject: [PATCH] Convert file format descriptions to rst Convert the old HTML files about file formats to reStructuredText, and merge them on a single page. This is more or less a blind conversion. No attempt is made to make them appear particularly nice, or to fix outdated information. But this works towards the goal of reducing the number of distinct document generation mechanisms, and should make it easier to restore functionality of linking to file formats from generated pages for programs. Now the only thing that remains in the old-html directory is the flowchart. Change-Id: I88bfbdf48f3ba870c9501ef933c03a947ea43635 --- docs/CMakeLists.txt | 2 + docs/conf.py | 18 - docs/old-html/online/cpt.html | 10 - docs/old-html/online/dat.html | 6 - docs/old-html/online/dlg.html | 29 - docs/old-html/online/edi.html | 9 - docs/old-html/online/edo.html | 11 - docs/old-html/online/edr.html | 6 - docs/old-html/online/ene.html | 12 - docs/old-html/online/eps.html | 9 - docs/old-html/online/files.html | 100 -- docs/old-html/online/g96.html | 22 - docs/old-html/online/gro.html | 69 - docs/old-html/online/hdb.html | 7 - docs/old-html/online/itp.html | 3 - docs/old-html/online/log.html | 4 - docs/old-html/online/m2p.html | 44 - docs/old-html/online/map.html | 23 - docs/old-html/online/mdp.html | 231 ---- docs/old-html/online/mtx.html | 7 - docs/old-html/online/ndx.html | 31 - docs/old-html/online/out.html | 5 - docs/old-html/online/pdb.html | 25 - docs/old-html/online/rtp.html | 83 -- docs/old-html/online/tex.html | 11 - docs/old-html/online/tng.html | 23 - docs/old-html/online/top.html | 92 -- docs/old-html/online/tpr.html | 20 - docs/old-html/online/trr.html | 20 - docs/old-html/online/xpm.html | 66 - docs/old-html/online/xtc.html | 97 -- docs/old-html/online/xvg.html | 9 - docs/online.rst | 1 - docs/user-guide/file-formats.rst | 1186 ++++++++++++++++- docs/user-guide/getting-started.rst | 30 +- .../images => user-guide}/plotje.gif | Bin docs/{old-html/images => user-guide}/xvgr.gif | Bin 37 files changed, 1200 insertions(+), 1121 deletions(-) delete mode 100644 docs/old-html/online/cpt.html delete mode 100644 docs/old-html/online/dat.html delete mode 100644 docs/old-html/online/dlg.html delete mode 100644 docs/old-html/online/edi.html delete mode 100644 docs/old-html/online/edo.html delete mode 100644 docs/old-html/online/edr.html delete mode 100644 docs/old-html/online/ene.html delete mode 100644 docs/old-html/online/eps.html delete mode 100644 docs/old-html/online/files.html delete mode 100644 docs/old-html/online/g96.html delete mode 100644 docs/old-html/online/gro.html delete mode 100644 docs/old-html/online/hdb.html delete mode 100644 docs/old-html/online/itp.html delete mode 100644 docs/old-html/online/log.html delete mode 100644 docs/old-html/online/m2p.html delete mode 100644 docs/old-html/online/map.html delete mode 100644 docs/old-html/online/mdp.html delete mode 100644 docs/old-html/online/mtx.html delete mode 100644 docs/old-html/online/ndx.html delete mode 100644 docs/old-html/online/out.html delete mode 100644 docs/old-html/online/pdb.html delete mode 100644 docs/old-html/online/rtp.html delete mode 100644 docs/old-html/online/tex.html delete mode 100644 docs/old-html/online/tng.html delete mode 100644 docs/old-html/online/top.html delete mode 100644 docs/old-html/online/tpr.html delete mode 100644 docs/old-html/online/trr.html delete mode 100644 docs/old-html/online/xpm.html delete mode 100644 docs/old-html/online/xtc.html delete mode 100644 docs/old-html/online/xvg.html rename docs/{old-html/images => user-guide}/plotje.gif (100%) rename docs/{old-html/images => user-guide}/xvgr.gif (100%) diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt index 3ebac52e2f..292bea2210 100644 --- a/docs/CMakeLists.txt +++ b/docs/CMakeLists.txt @@ -98,6 +98,8 @@ if (SPHINX_FOUND) 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}) diff --git a/docs/conf.py b/docs/conf.py index f501ee71be..3f6c600721 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -168,25 +168,7 @@ rst_epilog += """ .. _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 ---------------------------------------------- diff --git a/docs/old-html/online/cpt.html b/docs/old-html/online/cpt.html deleted file mode 100644 index 4ece4fc1c3..0000000000 --- a/docs/old-html/online/cpt.html +++ /dev/null @@ -1,10 +0,0 @@ -cpt file format -

Description

-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 gmx mdrun. diff --git a/docs/old-html/online/dat.html b/docs/old-html/online/dat.html deleted file mode 100644 index f7de6d513d..0000000000 --- a/docs/old-html/online/dat.html +++ /dev/null @@ -1,6 +0,0 @@ -dat file format -

Description

-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. diff --git a/docs/old-html/online/dlg.html b/docs/old-html/online/dlg.html deleted file mode 100644 index 7cbdbe376c..0000000000 --- a/docs/old-html/online/dlg.html +++ /dev/null @@ -1,29 +0,0 @@ -dlg file format -

Description

-The dlg file format is used as input for the -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"
-}
-
-}
-
diff --git a/docs/old-html/online/edi.html b/docs/old-html/online/edi.html deleted file mode 100644 index 4d619535de..0000000000 --- a/docs/old-html/online/edi.html +++ /dev/null @@ -1,9 +0,0 @@ -edi file format -

Description

-Files with the edi file extension contain information for -gmx mdrun -to run Molecular Dynamics with Essential Dynamics constraints. - - diff --git a/docs/old-html/online/edo.html b/docs/old-html/online/edo.html deleted file mode 100644 index ea4601ce8c..0000000000 --- a/docs/old-html/online/edo.html +++ /dev/null @@ -1,11 +0,0 @@ -edo file format -

Description

-Files with the edo file extension are generated by -gmx mdrun -if Molecular Dynamics is performed with Essential Dynamics -constraints. Depending on the parameters set in the -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. diff --git a/docs/old-html/online/edr.html b/docs/old-html/online/edr.html deleted file mode 100644 index e24fb87aea..0000000000 --- a/docs/old-html/online/edr.html +++ /dev/null @@ -1,6 +0,0 @@ -ene file format -

Description

-The edr file extension stands for portable energy file. -The energies are stored using the xdr protocol. -

-See also gmx energy. diff --git a/docs/old-html/online/ene.html b/docs/old-html/online/ene.html deleted file mode 100644 index a44e3dbebf..0000000000 --- a/docs/old-html/online/ene.html +++ /dev/null @@ -1,12 +0,0 @@ -ene file format -

Description

-The ene file extension stands for binary energy file. It holds the -energies as generated during your -gmx mdrun. -
-The file can be transformed to a portable energy file (portable -accross hardware platforms), the -.edr file using the program -gmx eneconv. -

-See also gmx energy. diff --git a/docs/old-html/online/eps.html b/docs/old-html/online/eps.html deleted file mode 100644 index 4aca8b1f63..0000000000 --- a/docs/old-html/online/eps.html +++ /dev/null @@ -1,9 +0,0 @@ -eps file format -

Description

-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 gmx xpm2ps program is -included below. It shows the secondary structure of a peptide as a function -of time. -

-hallo diff --git a/docs/old-html/online/files.html b/docs/old-html/online/files.html deleted file mode 100644 index e458217867..0000000000 --- a/docs/old-html/online/files.html +++ /dev/null @@ -1,100 +0,0 @@ -File formats -

-

Parameter files

-
-mdp -
run parameters, input for -gmx grompp and -gmx convert-tpr -
m2p -
input for gmx xpm2ps -
- -

Structure files

-
-
gro
GROMACS format -
g96
GROMOS-96 format -
pdb
brookhaven Protein DataBank format -
Generic structure formats: -gro, -g96, -pdb, or -tpr -
Structure+mass(db): -tpr, -gro, -g96 or -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

-
-
top
system topology (ascii) -
itp
include topology (ascii) -
rtp
residue topology (ascii) -
ndx
index file -
- -

Run Input files

-
-
tpr
system topology, parameters, coordinates -and velocities (binary, portable) -
Generic run input file formats: -tpr - -
- -

Trajectory files

-
-
tng
Any kind of data (compressed, portable, any precision) -
trr
x, v and f (binary, full precision, portable) -
xtc
x only (compressed, portable, any precision) -
gro
x and v (ascii, any precision) -
g96
x only (ascii, fixed high precision) -
pdb
x only (ascii, reduced precision) -
Formats for full-precision data: -tng or -trr -
Generic trajectory formats: -tng, -xtc, -trr, -gro, -g96, -pdb or -
- -

Energy files

-
-
ene
energies, temperature, pressure, box size, -density and virials (binary) -
edr
energies, temperature, pressure, box size, -density and virials (binary, portable) -
Generic energy formats: -edr or -ene -
- -

Other files

-
-
dat
generic, preferred for input -
edi -
essential dynamics constraints input for -gmx mdrun -
edo -
essential dynamics constraints output for -gmx mdrun -
eps
Encapsulated Postscript -
log
log file -
map
colormap input for -gmx do_dssp -
mtx
binary matrix data -
out
generic, preferred for output -
tex
LaTeX input -
xpm
ascii matrix data, use -gmx xpm2ps to convert to eps -
xvg
xvgr input -
-
diff --git a/docs/old-html/online/g96.html b/docs/old-html/online/g96.html deleted file mode 100644 index 2de14ff8a8..0000000000 --- a/docs/old-html/online/g96.html +++ /dev/null @@ -1,22 +0,0 @@ -g96 file format -

Description

-

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: -

-See the GROMOS-96 manual for a complete description of the blocks. -

-Note that all GROMACS programs can read compressed or g-zipped files. diff --git a/docs/old-html/online/gro.html b/docs/old-html/online/gro.html deleted file mode 100644 index 8f8af1f4b5..0000000000 --- a/docs/old-html/online/gro.html +++ /dev/null @@ -1,69 +0,0 @@ -gro file format -

Description

-

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): - - -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): - - - -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. diff --git a/docs/old-html/online/hdb.html b/docs/old-html/online/hdb.html deleted file mode 100644 index 8dfd3d877c..0000000000 --- a/docs/old-html/online/hdb.html +++ /dev/null @@ -1,7 +0,0 @@ -hdb file format -

Description

-The hdb file extension stands for hydrogen database -Such a file is needed by gmx pdb2gmx -when building hydrogen atoms that were either originally missing, or that -were removed with -ignh. - diff --git a/docs/old-html/online/itp.html b/docs/old-html/online/itp.html deleted file mode 100644 index 121a3a64bd..0000000000 --- a/docs/old-html/online/itp.html +++ /dev/null @@ -1,3 +0,0 @@ -itp file format -

Description

-The itp file extension stands for include toplogy. These files are included in topology files ( with the top extension ) diff --git a/docs/old-html/online/log.html b/docs/old-html/online/log.html deleted file mode 100644 index d9caeef915..0000000000 --- a/docs/old-html/online/log.html +++ /dev/null @@ -1,4 +0,0 @@ -log file format -

Description

-Logfiles are generated by some GROMACS programs and are usually in -human-readable format. Use more logfile. diff --git a/docs/old-html/online/m2p.html b/docs/old-html/online/m2p.html deleted file mode 100644 index 95986e09ef..0000000000 --- a/docs/old-html/online/m2p.html +++ /dev/null @@ -1,44 +0,0 @@ -m2p file format -

Description

-The m2p file format contains input options for the -gmx xpm2ps program. All of these options -are very easy to comprehend when you look at the PosScript(tm) output -from 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
-
diff --git a/docs/old-html/online/map.html b/docs/old-html/online/map.html deleted file mode 100644 index b2be65bd6a..0000000000 --- a/docs/old-html/online/map.html +++ /dev/null @@ -1,23 +0,0 @@ -map file format -

Description

-This file maps matrix data to RGB values which is used by the -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
-
diff --git a/docs/old-html/online/mdp.html b/docs/old-html/online/mdp.html deleted file mode 100644 index 7b66df25a6..0000000000 --- a/docs/old-html/online/mdp.html +++ /dev/null @@ -1,231 +0,0 @@ -mdp file format -

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 (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 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
-
diff --git a/docs/old-html/online/mtx.html b/docs/old-html/online/mtx.html deleted file mode 100644 index 6492e5db38..0000000000 --- a/docs/old-html/online/mtx.html +++ /dev/null @@ -1,7 +0,0 @@ -mtx file format -

Description

-Files with the mtx file extension contain a matrix. -The file format is identical to the trr format. -Currently this file format is only used for hessian matrices, -which are produced with gmx mdrun and read by -gmx nmeig. diff --git a/docs/old-html/online/ndx.html b/docs/old-html/online/ndx.html deleted file mode 100644 index 95766ab43e..0000000000 --- a/docs/old-html/online/ndx.html +++ /dev/null @@ -1,31 +0,0 @@ -ndx file format -

Description

-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 -(gmx view) -and by the preprocessor (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: -gmx make_ndx. diff --git a/docs/old-html/online/out.html b/docs/old-html/online/out.html deleted file mode 100644 index 0ca0157f86..0000000000 --- a/docs/old-html/online/out.html +++ /dev/null @@ -1,5 +0,0 @@ -out file format -

Description

-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. diff --git a/docs/old-html/online/pdb.html b/docs/old-html/online/pdb.html deleted file mode 100644 index a67c7ec26e..0000000000 --- a/docs/old-html/online/pdb.html +++ /dev/null @@ -1,25 +0,0 @@ -pdb file format -

Description

- -Files with the .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
-...
-...
-
diff --git a/docs/old-html/online/rtp.html b/docs/old-html/online/rtp.html deleted file mode 100644 index 84138a735b..0000000000 --- a/docs/old-html/online/rtp.html +++ /dev/null @@ -1,83 +0,0 @@ -rtp file format -

Description

-The rtp file extension stands for residue toplogy. -Such a file is needed by gmx pdb2gmx -to make a GROMACS topology for a protein contained in a .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 .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 .top file, -this is used for the GROMOS96 forcefield. -

-gmx pdb2gmx -automatically generates all angles, -this means that the [angles] field is only -useful for overriding .itp parameters. -

-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. -

-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
-
diff --git a/docs/old-html/online/tex.html b/docs/old-html/online/tex.html deleted file mode 100644 index 8d94f48339..0000000000 --- a/docs/old-html/online/tex.html +++ /dev/null @@ -1,11 +0,0 @@ -tex file format -

Description

-We use LaTeX for document processing. -Although the input is not so -user friendly, it has some advantages over word processors. - diff --git a/docs/old-html/online/tng.html b/docs/old-html/online/tng.html deleted file mode 100644 index a6b6c48e77..0000000000 --- a/docs/old-html/online/tng.html +++ /dev/null @@ -1,23 +0,0 @@ -tng file format -

Description

-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 gmx dump. -
-% gmx dump -f traj.tng
-
-or if you're not such a fast reader: -
-% gmxdump -f traj.tng | more
-
- -

-You can also get a quick look in the contents of the file (number of -frames etc.) using: -

-% gmx check -f traj.tng
-
diff --git a/docs/old-html/online/top.html b/docs/old-html/online/top.html deleted file mode 100644 index 67f6c174ff..0000000000 --- a/docs/old-html/online/top.html +++ /dev/null @@ -1,92 +0,0 @@ -top file format -

Description

-The top file extension stands for topology. It is an ascii file which is -read by gmx grompp which processes it -and creates a binary topology (.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
-
diff --git a/docs/old-html/online/tpr.html b/docs/old-html/online/tpr.html deleted file mode 100644 index 522032be51..0000000000 --- a/docs/old-html/online/tpr.html +++ /dev/null @@ -1,20 +0,0 @@ -tpr file format -

Description

-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: -
-% gmx dump -s topol.tpr
-
-or if you're not such a fast reader: -
-% gmxdump -s topol.tpr | more
-
- -

-You can also compare two tpr files using: -

-% gmx check -s1 top1 -s2 top2 | more
-
diff --git a/docs/old-html/online/trr.html b/docs/old-html/online/trr.html deleted file mode 100644 index b752ae0035..0000000000 --- a/docs/old-html/online/trr.html +++ /dev/null @@ -1,20 +0,0 @@ -trr file format -

Description

-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 gmx dump. -
-% gmx dump -f traj.trr
-
-or if you're not such a fast reader: -
-% gmxdump -f traj.trr | more
-
- -

-You can also get a quick look in the contents of the file (number of -frames etc.) using: -

-% gmx check -f traj.trr
-
diff --git a/docs/old-html/online/xpm.html b/docs/old-html/online/xpm.html deleted file mode 100644 index ffe22df145..0000000000 --- a/docs/old-html/online/xpm.html +++ /dev/null @@ -1,66 +0,0 @@ -xpm file format -

Description

-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 -gmx xpm2ps. -The optional extra field are: - -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"
-
diff --git a/docs/old-html/online/xtc.html b/docs/old-html/online/xtc.html deleted file mode 100644 index acf2c52b1c..0000000000 --- a/docs/old-html/online/xtc.html +++ /dev/null @@ -1,97 +0,0 @@ -xtc file format -

Description

-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 xdr library is extended with a special routine -to write 3-D float coordinates. -

-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
-      
- 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
-
-To link your program use -L$(GMXHOME)/lib/$(CPU) -lxtcf -on your linker command line. -The source for this test can be found in file -$(GMXHOME)/src/gmxlib/testxtcf.f. diff --git a/docs/old-html/online/xvg.html b/docs/old-html/online/xvg.html deleted file mode 100644 index c577934624..0000000000 --- a/docs/old-html/online/xvg.html +++ /dev/null @@ -1,9 +0,0 @@ -xvgr file format -

Description

-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.

-xvgr window
diff --git a/docs/online.rst b/docs/online.rst index 7b683e4f22..041e1fbf4d 100644 --- a/docs/online.rst +++ b/docs/online.rst @@ -2,4 +2,3 @@ Online reference ================ * `Flow Chart `_ -* `File Formats `_ diff --git a/docs/user-guide/file-formats.rst b/docs/user-guide/file-formats.rst index 9269f7517c..667ff7284b 100644 --- a/docs/user-guide/file-formats.rst +++ b/docs/user-guide/file-formats.rst @@ -1,6 +1,1186 @@ 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 WEDSAM which uses + output from the programs in the ESSDYN menu of the + WHAT IF 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 xdr 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 this link. + +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 diff --git a/docs/user-guide/getting-started.rst b/docs/user-guide/getting-started.rst index b6171209b4..d35bf01b99 100644 --- a/docs/user-guide/getting-started.rst +++ b/docs/user-guide/getting-started.rst @@ -47,7 +47,7 @@ Molecular Topology file (``.top``) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 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. @@ -56,11 +56,11 @@ Molecular Structure file (``.gro``, ``.pdb``) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 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 @@ -73,11 +73,11 @@ topology. 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 ` +is available. Index file (``.ndx``) ^^^^^^^^^^^^^^^^^^^^^ @@ -90,12 +90,12 @@ not consider the use of index files. 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``) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -104,9 +104,9 @@ Once the run input file is available, we can start the simulation. The 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 ----------------- diff --git a/docs/old-html/images/plotje.gif b/docs/user-guide/plotje.gif similarity index 100% rename from docs/old-html/images/plotje.gif rename to docs/user-guide/plotje.gif diff --git a/docs/old-html/images/xvgr.gif b/docs/user-guide/xvgr.gif similarity index 100% rename from docs/old-html/images/xvgr.gif rename to docs/user-guide/xvgr.gif -- 2.22.0