From 74e05a68cda28e433f549745a7b0021396f20da8 Mon Sep 17 00:00:00 2001 From: anton Date: Mon, 29 Nov 1999 12:38:07 +0000 Subject: [PATCH] fixed layout and link consistency --- share/html/online/getting_started.html | 300 +++++++++++++++++---------------- 1 file changed, 159 insertions(+), 141 deletions(-) diff --git a/share/html/online/getting_started.html b/share/html/online/getting_started.html index a7e913bf3c..0fabadde52 100644 --- a/share/html/online/getting_started.html +++ b/share/html/online/getting_started.html @@ -1,9 +1,4 @@ - Getting Started @@ -58,9 +53,9 @@ Dynamics and familiar with Unix, including the use of a text editor such as emacs or vi. We furthermore assume the software is installed properly on your system. When you see a line like -

+

 % ls -l 
-

+
you are supposed to type the contents of that line (not the %) on your computer. @@ -74,24 +69,24 @@ Groningen MD group.

Setting up your environment

Edit your .cshrc file to include the following statement: -

+

 source ~gmx/GMXRC
-

+
which has some (system dependent) PATH settings etcetera. Then type -

+

 % source ~gmx/GMXRC
-

+
to start right away, or, alternatively log off and on again to automatically source the environment.

Check if you now have the proper environment by -

+

 % echo $GMXHOME
-

+
It should read something like: -

+

 /home/gmx/gmx2.0
-

+
This is the directory in which the binaries and library files live. If you see nothing (a blank line) something is wrong with the installation, check with your system manager, or (if @@ -104,22 +99,22 @@ files, to your own directory. Chdir to the directory you want to put the examples directory. This directory (named tutor) will need about 20 MB of disk space, when it is completely filled. -

-% cd ``your own directory'' -

+
+% cd ``your own directory''
+
then copy the examples: -

+

 % cp -r ~gmx/home2.0/tutor .
-
 
+
(NOTE: include the ``.'') You now have a subdirectory tutor. Move there -

+

 % cd tutor
-
 
+
and view the contents of this directory -

+

 % ls -l
-
 
+
If all is well you will have five subdirectories with examples with names like gmxdemo, nmr1, nmr2, speptide and water. @@ -134,26 +129,32 @@ the online manual while you are browsing through the examples.

The demo is designed to demonstrate the user-friendlyness of the GROMACS software package. Start the demo by going to your tutor/gmxdemo directory: -

+

 % cd tutor/gmxdemo
-
 Start the demo: 
-

+
Start the demo: +
 % demo
-

+
This demo handles a complete Molecular Dynamics simulation of a peptide in water, starting from a pdb structure. When you run a Molecular Dynamics simulation with GROMACS you will encounter the following file formats: -

Molecular Topology file (.top)

+
+
+Molecular Topology file (.top) +
The molecular topology file is generated by the program pdb2gmx. pdb2gmx translates a 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. +

-

Molecular Structure file (.gro, .pdb)

+
+Molecular Structure file (.gro, .pdb) +
When the pdb2gmx program is executed to generate a molecular topology, it also translates the structure file (.pdb file) to a gromos @@ -172,22 +173,31 @@ case water). The output of genbox is a gromos the peptide dissolved in water. The genbox program also changes the molecular topology file (generated by pdb2gmx) to add solvent to the topology. +

-

Molecular Dynamics parameter file (.mdp)

+
+Molecular Dynamics parameter file (.mdp) +
The Molecular Dynamics Parameter (.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 +easiest way of handling such a file is by adapting a sample .mdp file. A sample mdp file can be found online. +

-

Index file (.ndx)

+
+Index file (.ndx) +
Sometimes you may need an index file to specify actions on groups of atoms (e.g. Temperature coupling, accelerations, freezing). Usually the default ibdex groups will be sufficient, so for this demo we will not consider the use of index files. +

-

Run input file (.tpr)

+
+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 @@ -196,11 +206,12 @@ index file (ndx) to generate a run input file (< This file contains all information needed to start a simulation with GROMACS. The grompp program processes all input files and generates the run input -tpr file. - -

Trajectory file -(.trr)

+.tpr file. +

+
+Trajectory file (.trr) +
Once the run input file is available, we can start the simulation. The program which starts the simulation is called mdrun. The only input file @@ -210,7 +221,10 @@ The output files of mdrun are the trajectory file (.trr file or .trj if you don't have XDR) and a logfile ( -.log file).

+.log file). +

+ +


@@ -221,65 +235,74 @@ in a rectangular box. In this example the GROMACS software team already generated most of the neccesary input files. The files needed in this example are:

Change your directory to tutor/water : -

+

 % cd tutor/water
-

+
Let's first have a look at the coordinate file: -

-% more spc216.gro -

+
+% more spc216.gro
+
Or to view the water box graphically: -

-% rasmol spc216.pdb -

+
+% rasmol spc216.pdb 
+
Have a look at the topology file: -

-% more water.top -

+
+% more water.top
+
Have a look at the MD-parameters file: -

-% more water.mdp -

+
+% more water.mdp
+
Since all the neccesary files are available, we are going to, preprocess all the input files to create a run input -(tpr) file. +(.tpr) file. This run input file is the only input file for the MD-program mdrun. -

-% grompp -f water -p water -c spc216.gro -o water -

+
+% grompp -f water.mdp -p water.top -c spc216.gro -o water.tpr
+
The run input file is only viewable with the program gmxdump. In this way it is possible to check if the preprocessor grompp worked well. -

-% gmxdump -s water.tpr | more -

+
+% gmxdump -s water.tpr | more
+
Now it's time to start to the simulation -

-% mdrun -s water.tpr -o water.trr -c water_out.gro -v -g mdlog -

+
+% mdrun -s water.tpr -o water.trr -c water_out.gro -v -g water.log
+
After the MD simulation is finished, it is possible to view the trajectory with the ngmx program: -

+

 % ngmx -f water.trr -s water.tpr
-

+
+

+When the program starts, you must select a group of atoms to view. In +our case that will be "SOL" (for solvent) or "System", which is the +same for a box of water as we have. Select one and click OK. Then +select Display->Animate from the menu. Use the buttons to see your +water moving (note: "Play" steps one frame forward; "Fast Forward" +plays; "Rewind" skips back to the beginning of the trajectory). +

+ Calculate a radial distribution function of the Oxygen atoms. The -index file oxygen.ndx +index file oxygen.ndx contains one group with all the oxygen atoms. -

-% g_rdf -f water.trr -n oxygen.ndx -o rdf.xvg -s water.tpr -

+
+% g_rdf -f water.trr -n oxygen.ndx -o rdf.xvg -s water.tpr
+
view the output graph of g_rdf -

-% xvgr rdf.xvg -

+
+% xvgr rdf.xvg 
+
Which shows you the radial distribution function for Oxygen-Oxygen in SPC water.

@@ -303,22 +326,22 @@ To be able to simulate the S-Peptide we need a starting structure. This can be taken from the protein data bank. There are a number of different structure for Ribonuclease S, from one of which we have cut out the first 20 residues, and stored it in -speptide.pdb. +speptide.pdb. Have a look at the file -

-% more speptide.pdb -

+
+% more speptide.pdb
+
If you have access to a molecular graphics program such as rasmol, xmol, or a commercial package, you can look at the molecule on screen, eg: -

-% rasmol speptide.pdb -

+
+% rasmol speptide.pdb
+
The following steps have to be taken to perform a simulation of the peptide.
    -
  1. Convert the pdb-file speptide.pdb +
  2. Convert the pdb-file speptide.pdb to a GROMACS structure file and a GROMACS topology file.
  3. Solvate the peptide in water
  4. Perform an energy minimization of the peptide in solvent @@ -332,49 +355,45 @@ We will describe in detail how such a simulation can be done, starting from a pdb-file.

    -Generate a topology file (top) from the pdb-file (pdb) +Generate a topology file (.top) from the pdb-file (.pdb)

    Generate a molecular topology and a structure file in format. This can be done with the pdb2gmx program: -

    +

     % pdb2gmx -f speptide.pdb -p speptide.top -o speptide.gro
-
    
+
    Note that the correct file extension are added automatically to the filenames on the command line. You will only be asked to choose a forcefield, choose 0, but you can also have pdb2gmx ask you about protonation of residues, and about protonation of N- and C-terminus. You can type -

    +

     % pdb2gmx -h
-
    
+
    to see the available options.

    The pdb2gmx program has generated a topology file speptide.top and a -GROMACS structure file speptide.gro and it will +GROMACS structure file speptide.gro and it will generate hydrogen positions. The -p and -o options with he filenames are optional; without them the files topol.top and conf.gro will be generated. Now have a look at the output from pdb2gmx, -

    +

     % more speptide.gro
-
    
+
    You will see a close resemblance to the pdb file, only the layout of -the file is a bit different. For the exact layout check -gro.html. +the file is a bit different. Also do have a look at the topology -

    +

     % more speptide.top
-
    
+
    You will see a large file containing the atom types, the physical -bonds between atoms, etcetera. If you want to know more about -the topology file read -top.html. - +bonds between atoms, etcetera.

    Solvate the peptide in a periodic box filled with water

    @@ -386,10 +405,10 @@ will make a rectangular box with empty space of user specified size around the molecule. genbox will read the structure file and fill the box with water. -

    +

     % editconf -f speptide -o -dc 0.5
    
 % genbox -cp out -cs -p speptide -o b4em
-
    
+
    The program prints some lines of user information, like the volume of the box and the number of water molecules added to your peptide. genbox @@ -398,9 +417,9 @@ also changes the topology file these water molecules in the topology. This can been seen by looking at the bottom of the speptide.top file -

    +

     % tail speptide.top
-
    
+
    You will see some lines like 
     [ system ]
@@ -426,9 +445,9 @@ can be generated using make_ndx.
 This is an interactive program that lets you manipulate molecules,
 residues and atom. It's use should be self-explanatory.  To invoke the
 program you would
-
    
+
     % make_ndx -f b4em
-
    
+
    
 but don't bother for now.
 
 
    Perform an energy minimization of the peptide in solvent
    
@@ -444,28 +463,27 @@ however, we have to preprocess the topology file (
 speptide.top), the
 structure file (
 speptide.gro) and a
-special parameter file (
-em.mdp). Check
+special parameter file (em.mdp). Check
 the contents of this file 
-
    
-% more em.mdp
-
    
+
    +% more em.mdp
+
    
 Preprocessing is done with the preprocessor called 
 grompp. This reads
 up the files just mentioned:
 
-
    
+
     % grompp -v -f em -c b4em -o em -p speptide
-
    
+
    
 In this command the -v option turns on verbose mode, which
 gives a little bit of clarifying info on what the program is doing.
-We now have made a run input file (em.tpr) which
+We now have made a run input file (em.tpr) which
 serves as input for the 
 mdrun program. Now
 we can do the energy minimization:
-
    
+
     % mdrun -v -s em -o em -c after_em -g emlog
-
    
+
    
 In this command the -v option turns on verbose mode again.
 The -o option sets the filename for the trajectory file,
 which is not very important in energy minimizations. The -c
@@ -505,60 +523,60 @@ describing which atoms are to be restrained. Such a section is
 actually generated by the 
 pdb2gmx program. In the
 topology file it looks like
-
    
+
     #ifdef POSRES
    
 #include "posres.itp"
    
 #endif
-
    
+
    
 In the topology file we use
 conditional inclusion, i.e. only if a variable POSRES is set
 in the preprocessor do we include the file, this allows us to use the
 same topology file for runs with and without position restraints. In
-the pr.mdp parameter file 
+the pr.mdp parameter file 
 for the position restraints this variable is set indeed:
-
    
+
     define              =  -DPOSRES
-
    
+
    
 
    
 At last we can generate the input for the position restrained mdrun:
-
    
+
     % grompp -f pr -o pr -c after_em -r after_em -p speptide
-
    
+
    
 Now it's MDrun time:
-
    
+
     % mdrun -v -s pr -e pr -o pr -c after_pr -g prlog >& pr.job &
-
    
+
    
 This run is started in the background (it will take a while), you
 can watch how long it will take by typing:
-
    
+
     % tail -f pr.job
-
    
+
    
 With the Ctrl-C key you can kill the tail command.
 A good check of your simulation is to see whether density and potential
 energies have converged:
-
    
+
     % g_energy -f pr -o out -w
-
    
+
    
 The 
 g_energy program will prompt you to select a number of energy terms
 from a list. For potential energy type:
-
    
+
     9 0
-
    
+
    
 If you have the xmgr program installed it will automatically pop up on your
 screen with the energy plot. You can do the same for the density
 and other energy terms, such as Solvent-Protein interactions.
 
 
    Perform full MD without restraints
    
 Full MD is very similar to the restrained MD as far as GROMACS is
-concerned. Check out the full.mdp for details.
-
    
+concerned. Check out the full.mdp for details.
+
     % grompp -v -f full -o full -c after_pr -p speptide
-
    
+
    
 Then we can start mdrunning
-
    
+
     % mdrun -v -s full -e full -o full -c after_full -g flog >& full.job &
-
    
+
    
 You should do similar convergence checks (and more!) as for the position
 restrained simulation.
 
@@ -606,18 +624,18 @@ For other systemd (eg. pure liquids or mixtures) one needs:
 
  5.  	The atomic coordinates, which can be generated by a variety of 
 	interactive programs (eg. Quanta, Cerius, HyperChem). 
 	Coordinate files can be exported in pdb-format and 
-	converted to .gro format by 
+	converted to .gro format by 
 	the editconf program:
-	
    
+	
     % editconf -f conf.pdb -o conf.gro
-	
    
+	
    
 	where conf.gro is the  coordinatefile, 
 	or converted back to pdb-format by
-	
    
+	
     % editconf -f conf.gro -o conf.pdb
-	
    
+	
    
 	where conf is a file with  coordinates, and 
-	conf.pdb is the target file in .pdb format.
+	conf.pdb is the target file in .pdb format.
 	NOTE: Make sure that the graphics programs export 
 	whole molecules instead of molecules that are cut in pieces
 	(due to the periodic boundary conditions)
-- 
2.11.4.GIT